NIPS 2023 papers

We study the problem of learning causal representations from unknown, latent interventions in a general setting, where the latent distribution is Gaussian but the mixing function is completely general. We prove strong identifiability results given unknown single-node interventions, i.e., without having access to the intervention targets. This generalizes prior works which have focused on weaker classes, such as linear maps or paired counterfactual data. This is also the first instance of identifiability from non-paired interventions for deep neural network embeddings and general causal structures. Our proof relies on carefully uncovering the high-dimensional geometric structure present in the data distribution after a non-linear density transformation, which we capture by analyzing quadratic forms of precision matrices of the latent distributions. Finally, we propose a contrastive algorithm to identify the latent variables in practice and evaluate its performance on various tasks.

Some of the most successful knowledge graph embedding (KGE) models for link prediction – CP, RESCAL, TuckER, ComplEx – can be interpreted as energy-based models. Under this perspective they are not amenable for exact maximum-likelihood estimation (MLE), sampling and struggle to integrate logical constraints. This work re-interprets the score functions of these KGEs as circuits – constrained computational graphs allowing efficient marginalisation. Then, we design two recipes to obtain efficient generative circuit models by either restricting their activations to be non-negative or squaring their outputs. Our interpretation comes with little or no loss of performance for link prediction, while the circuits framework unlocks exact learning by MLE, efficient sampling of new triples, and guarantee that logical constraints are satisfied by design. Furthermore, our models scale more gracefully than the original KGEs on graphs with millions of entities.

We tackle the problems of latent variables identification and "out-of-support'' image generation in representation learning. We show that both are possible for a class of decoders that we call additive, which are reminiscent of decoders used for object-centric representation learning (OCRL) and well suited for images that can be decomposed as a sum of object-specific images. We provide conditions under which exactly solving the reconstruction problem using an additive decoder is guaranteed to identify the blocks of latent variables up to permutation and block-wise invertible transformations. This guarantee relies only on very weak assumptions about the distribution of the latent factors, which might present statistical dependencies and have an almost arbitrarily shaped support. Our result provides a new setting where nonlinear independent component analysis (ICA) is possible and adds to our theoretical understanding of OCRL methods. We also show theoretically that additive decoders can generate novel images by recombining observed factors of variations in novel ways, an ability we refer to as Cartesian-product extrapolation. We show empirically that additivity is crucial for both identifiability and extrapolation on simulated data.

Gaussian processes are a powerful framework for quantifying uncertainty and for sequential decision-making but are limited by the requirement of solving linear systems. In general, this has a cubic cost in dataset size and is sensitive to conditioning. We explore stochastic gradient algorithms as a computationally efficient method of approximately solving these linear systems: we develop low-variance optimization objectives for sampling from the posterior and extend these to inducing points. Counterintuitively, stochastic gradient descent often produces accurate predictions, even in cases where it does not converge quickly to the optimum. We explain this through a spectral characterization of the implicit bias from non-convergence. We show that stochastic gradient descent produces predictive distributions close to the true posterior both in regions with sufficient data coverage, and in regions sufficiently far away from the data. Experimentally, stochastic gradient descent achieves state-of-the-art performance on sufficiently large-scale or ill-conditioned regression tasks. Its uncertainty estimates match the performance of significantly more expensive baselines on a large-scale Bayesian~optimization~task.

In this work, we deepen on the use of normalizing flows for causal reasoning. Specifically, we first leverage recent results on non-linear ICA to show that causal models are identifiable from observational data given a causal ordering, and thus can be recovered using autoregressive normalizing flows (NFs). Second, we analyze different design and learning choices for *causal normalizing flows* to capture the underlying causal data-generating process. Third, we describe how to implement the *do-operator* in causal NFs, and thus, how to answer interventional and counterfactual questions. Finally, in our experiments, we validate our design and training choices through a comprehensive ablation study; compare causal NFs to other approaches for approximating causal models; and empirically demonstrate that causal NFs can be used to address real-world problems—where the presence of mixed discrete-continuous data and partial knowledge on the causal graph is the norm. The code for this work can be found at https://github.com/psanch21/causal-flows.

We present an exact Bayesian inference method for discrete statistical models, which can find exact solutions to a large class of discrete inference problems, even with infinite support and continuous priors. To express such models, we introduce a probabilistic programming language that supports discrete and continuous sampling, discrete observations, affine functions, (stochastic) branching, and conditioning on discrete events. Our key tool is *probability generating functions*: they provide a compact closed-form representation of distributions that are definable by programs, thus enabling the exact computation of posterior probabilities, expectation, variance, and higher moments. Our inference method is provably correct and fully automated in a tool called *Genfer*, which uses automatic differentiation (specifically, Taylor polynomials), but does not require computer algebra. Our experiments show that Genfer is often faster than the existing exact inference tools PSI, Dice, and Prodigy. On a range of real-world inference problems that none of these exact tools can solve, Genfer's performance is competitive with approximate Monte Carlo methods, while avoiding approximation errors.

We establish the first mathematically rigorous link between Bayesian, variational Bayesian, and ensemble methods. A key step towards this it to reformulate the non-convex optimisation problem typically encountered in deep learning as a convex optimisation in the space of probability measures. On a technical level, our contribution amounts to studying generalised variational inference through the lense of Wasserstein gradient flows. The result is a unified theory of various seemingly disconnected approaches that are commonly used for uncertainty quantification in deep learning---including deep ensembles and (variational) Bayesian methods. This offers a fresh perspective on the reasons behind the success of deep ensembles over procedures based on parameterised variational inference, and allows the derivation of new ensembling schemes with convergence guarantees. We showcase this by proposing a family of interacting deep ensembles with direct parallels to the interactions of particle systems in thermodynamics, and use our theory to prove the convergence of these algorithms to a well-defined global minimiser on the space of probability measures.

We propose a novel neural algorithm for the fundamental problem of computing the entropic optimal transport (EOT) plan between probability distributions which are accessible by samples. Our algorithm is based on the saddle point reformulation of the dynamic version of EOT which is known as the Schrödinger Bridge problem. In contrast to the prior methods for large-scale EOT, our algorithm is end-to-end and consists of a single learning step, has fast inference procedure, and allows handling small values of the entropy regularization coefficient which is of particular importance in some applied problems. Empirically, we show the performance of the method on several large-scale EOT tasks. The code for the ENOT solver can be found at https://github.com/ngushchin/EntropicNeuralOptimalTransport

Causality is a central concept in a wide range of research areas, yet there is still no universally agreed axiomatisation of causality. We view causality both as an extension of probability theory and as a study of what happens when one intervenes on a system, and argue in favour of taking Kolmogorov's measure-theoretic axiomatisation of probability as the starting point towards an axiomatisation of causality. To that end, we propose the notion of a causal space, consisting of a probability space along with a collection of transition probability kernels, called causal kernels, that encode the causal information of the space. Our proposed framework is not only rigorously grounded in measure theory, but it also sheds light on long-standing limitations of existing frameworks including, for example, cycles, latent variables and stochastic processes.

In many real-world scenarios it is crucial to be able to reliably and efficiently reason under uncertainty while capturing complex relationships in data. Probabilistic circuits (PCs), a prominent family of tractable probabilistic models, offer a remedy to this challenge by composing simple, tractable distributions into a high-dimensional probability distribution. However, learning PCs on heterogeneous data is challenging and densities of some parametric distributions are not available in closed form, limiting their potential use. We introduce characteristic circuits (CCs), a family of tractable probabilistic models providing a unified formalization of distributions over heterogeneous data in the spectral domain. The one-to-one relationship between characteristic functions and probability measures enables us to learn high-dimensional distributions on heterogeneous data domains and facilitates efficient probabilistic inference even when no closed-form density function is available. We show that the structure and parameters of CCs can be learned efficiently from the data and find that CCs outperform state-of-the-art density estimators for heterogeneous data domains on common benchmark data sets.

Nonlinear independent component analysis (ICA) aims to uncover the true latent sources from their observable nonlinear mixtures. Despite its significance, the identifiability of nonlinear ICA is known to be impossible without additional assumptions. Recent advances have proposed conditions on the connective structure from sources to observed variables, known as Structural Sparsity, to achieve identifiability in an unsupervised manner. However, the sparsity constraint may not hold universally for all sources in practice. Furthermore, the assumptions of bijectivity of the mixing process and independence among all sources, which arise from the setting of ICA, may also be violated in many real-world scenarios. To address these limitations and generalize nonlinear ICA, we propose a set of new identifiability results in the general settings of undercompleteness, partial sparsity and source dependence, and flexible grouping structures. Specifically, we prove identifiability when there are more observed variables than sources (undercomplete), and when certain sparsity and/or source independence assumptions are not met for some changing sources. Moreover, we show that even in cases with flexible grouping structures (e.g., part of the sources can be divided into irreducible independent groups with various sizes), appropriate identifiability results can also be established. Theoretical claims are supported empirically on both synthetic and real-world datasets.

In variational inference, the benefits of Bayesian models rely on accurately capturing the true posterior distribution. We propose using neural samplers that specify implicit distributions, which are well-suited for approximating complex multimodal and correlated posteriors in high-dimensional spaces. Our approach introduces novel bounds for approximate inference using implicit distributions by locally linearising the neural sampler. This is distinct from existing methods that rely on additional discriminator networks and unstable adversarial objectives. Furthermore, we present a new sampler architecture that, for the first time, enables implicit distributions over tens of millions of latent variables, addressing computational concerns by using differentiable numerical approximations. We empirically show that our method is capable of recovering correlations across layers in large Bayesian neural networks, a property that is crucial for a network's performance but notoriously challenging to achieve. To the best of our knowledge, no other method has been shown to accomplish this task for such large models. Through experiments in downstream tasks, we demonstrate that our expressive posteriors outperform state-of-the-art uncertainty quantification methods, validating the effectiveness of our training algorithm and the quality of the learned implicit approximation.

Solving the quantum many-body Schrödinger equation is a fundamental and challenging problem in the fields of quantum physics, quantum chemistry, and material sciences. One of the common computational approaches to this problem is Quantum Variational Monte Carlo (QVMC), in which ground-state solutions are obtained by minimizing the energy of the system within a restricted family of parameterized wave functions. Deep learning methods partially address the limitations of traditional QVMC by representing a rich family of wave functions in terms of neural networks. However, the optimization objective in QVMC remains notoriously hard to minimize and requires second-order optimization methods such as natural gradient. In this paper, we first reformulate energy functional minimization in the space of Born distributions corresponding to particle-permutation (anti-)symmetric wave functions, rather than the space of wave functions. We then interpret QVMC as the Fisher--Rao gradient flow in this distributional space, followed by a projection step onto the variational manifold. This perspective provides us with a principled framework to derive new QMC algorithms, by endowing the distributional space with better metrics, and following the projected gradient flow induced by those metrics. More specifically, we propose ``Wasserstein Quantum Monte Carlo'' (WQMC), which uses the gradient flow induced by the Wasserstein metrics, rather than Fisher--Rao metric, and corresponds to *transporting* the probability mass, rather than *teleporting* it. We demonstrate empirically that the dynamics of WQMC results in faster convergence to the ground state of molecular systems.

Quantifying variable importance is essential for answering high-stakes questions in fields like genetics, public policy, and medicine. Current methods generally calculate variable importance for a given model trained on a given dataset. However, for a given dataset, there may be many models that explain the target outcome equally well; without accounting for all possible explanations, different researchers may arrive at many conflicting yet equally valid conclusions given the same data. Additionally, even when accounting for all possible explanations for a given dataset, these insights may not generalize because not all good explanations are stable across reasonable data perturbations. We propose a new variable importance framework that quantifies the importance of a variable across the set of all good models and is stable across the data distribution. Our framework is extremely flexible and can be integrated with most existing model classes and global variable importance metrics. We demonstrate through experiments that our framework recovers variable importance rankings for complex simulation setups where other methods fail. Further, we show that our framework accurately estimates the _true importance_ of a variable for the underlying data distribution. We provide theoretical guarantees on the consistency and finite sample error rates for our estimator. Finally, we demonstrate its utility with a real-world case study exploring which genes are important for predicting HIV load in persons with HIV, highlighting an important gene that has not previously been studied in connection with HIV.

Cooperative communication plays a fundamental role in theories of human-human interaction--cognition, culture, development, language, etc.--as well as human-robot interaction. The core challenge in cooperative communication is the problem of common ground: having enough shared knowledge and understanding to successfully communicate. Prior models of cooperative communication, however, uniformly assume the strongest form of common ground, perfect and complete knowledge sharing, and, therefore, fail to capture the core challenge of cooperative communication. We propose a general theory of cooperative communication that is mathematically principled and explicitly defines a spectrum of common ground possibilities, going well beyond that of perfect and complete knowledge sharing, on spaces that permit arbitrary representations of data and hypotheses. Our framework is a strict generalization of prior models of cooperative communication. After considering a parametric form of common ground and viewing the data selection and hypothesis inference processes of communication as encoding and decoding, we establish a connection to variational autoencoding, a powerful model in modern machine learning. Finally, we carry out a series of empirical simulations to support and elaborate on our theoretical results.

In this paper we offer a new perspective on the well established agglomerative clustering algorithm, focusing on recovery of hierarchical structure. We recommend a simple variant of the standard algorithm, in which clusters are merged by maximum average dot product and not, for example, by minimum distance or within-cluster variance. We demonstrate that the tree output by this algorithm provides a bona fide estimate of generative hierarchical structure in data, under a generic probabilistic graphical model. The key technical innovations are to understand how hierarchical information in this model translates into tree geometry which can be recovered from data, and to characterise the benefits of simultaneously growing sample size and data dimension. We demonstrate superior tree recovery performance with real data over existing approaches such as UPGMA, Ward's method, and HDBSCAN.

Normalizing flow is a class of deep generative models for efficient sampling and likelihood estimation, which achieves attractive performance, particularly in high dimensions. The flow is often implemented using a sequence of invertible residual blocks. Existing works adopt special network architectures and regularization of flow trajectories. In this paper, we develop a neural ODE flow network called JKO-iFlow, inspired by the Jordan-Kinderleherer-Otto (JKO) scheme, which unfolds the discrete-time dynamic of the Wasserstein gradient flow. The proposed method stacks residual blocks one after another, allowing efficient block-wise training of the residual blocks, avoiding sampling SDE trajectories and score matching or variational learning, thus reducing the memory load and difficulty in end-to-end training. We also develop adaptive time reparameterization of the flow network with a progressive refinement of the induced trajectory in probability space to improve the model accuracy further. Experiments with synthetic and real data show that the proposed JKO-iFlow network achieves competitive performance compared with existing flow and diffusion models at a significantly reduced computational and memory cost.

A single panel of a comic book can say a lot: it can depict not only where the characters currently are, but also their motions, their motivations, their emotions, and what they might do next. More generally, humans routinely infer complex sequences of past and future events from a *static snapshot* of a *dynamic scene*, even in situations they have never seen before. In this paper, we model how humans make such rapid and flexible inferences. Building on a long line of work in cognitive science, we offer a Monte Carlo algorithm whose inferences correlate well with human intuitions in a wide variety of domains, while only using a small, cognitively-plausible number of samples. Our key technical insight is a surprising connection between our inference problem and Monte Carlo path tracing, which allows us to apply decades of ideas from the computer graphics community to this seemingly-unrelated theory of mind task.

High-dimensional mediation analysis is often associated with a multiple testing problem for detecting significant mediators. Assessing the uncertainty of this detecting process via false discovery rate (FDR) has garnered great interest. To control the FDR in multiple testing, two essential steps are involved: ranking and selection. Existing approaches either construct p-values without calibration or disregard the joint information across tests, leading to conservation in FDR control or non-optimal ranking rules for multiple hypotheses. In this paper, we develop an adaptive mediation detection procedure (referred to as "AMDP") to identify relevant mediators while asymptotically controlling the FDR in high-dimensional mediation analysis. AMDP produces the optimal rule for ranking hypotheses and proposes a data-driven strategy to determine the threshold for mediator selection. This novel method captures information from the proportions of composite null hypotheses and the distribution of p-values, which turns the high dimensionality into an advantage instead of a limitation. The numerical studies on synthetic and real data sets illustrate the performances of AMDP compared with existing approaches.

Interpreting time series models is uniquely challenging because it requires identifying both the location of time series signals that drive model predictions and their matching to an interpretable temporal pattern. While explainers from other modalities can be applied to time series, their inductive biases do not transfer well to the inherently challenging interpretation of time series. We present TimeX, a time series consistency model for training explainers. TimeX trains an interpretable surrogate to mimic the behavior of a pretrained time series model. It addresses the issue of model faithfulness by introducing model behavior consistency, a novel formulation that preserves relations in the latent space induced by the pretrained model with relations in the latent space induced by TimeX. TimeX provides discrete attribution maps and, unlike existing interpretability methods, it learns a latent space of explanations that can be used in various ways, such as to provide landmarks to visually aggregate similar explanations and easily recognize temporal patterns. We evaluate TimeX on eight synthetic and real-world datasets and compare its performance against state-of-the-art interpretability methods. We also conduct case studies using physiological time series. Quantitative evaluations demonstrate that TimeX achieves the highest or second-highest performance in every metric compared to baselines across all datasets. Through case studies, we show that the novel components of TimeX show potential for training faithful, interpretable models that capture the behavior of pretrained time series models.

Since its inception in 1982, Oja's algorithm has become an established method for streaming principle component analysis (PCA). We study the problem of streaming PCA, where the data-points are sampled from an irreducible, aperiodic, and reversible Markov chain starting in stationarity. Our goal is to estimate the top eigenvector of the unknown covariance matrix of the stationary distribution. This setting has implications in scenarios where data can solely be sampled from a Markov Chain Monte Carlo (MCMC) type algorithm, and the objective is to perform inference on parameters of the stationary distribution. Most convergence guarantees for Oja's algorithm in the literature assume that the data-points are sampled IID. For data streams with Markovian dependence, one typically downsamples the data to get a "nearly" independent data stream. In this paper, we obtain the first near-optimal rate for Oja's algorithm on the entire data, where we remove the logarithmic dependence on the sample size, $n$, resulting from throwing data away in downsampling strategies.

We propose novel statistics which maximise the power of a two-sample test based on the Maximum Mean Discrepancy (MMD), by adapting over the set of kernels used in defining it. For finite sets, this reduces to combining (normalised) MMD values under each of these kernels via a weighted soft maximum. Exponential concentration bounds are proved for our proposed statistics under the null and alternative. We further show how these kernels can be chosen in a data-dependent but permutation-independent way, in a well-calibrated test, avoiding data splitting. This technique applies more broadly to general permutation-based MMD testing, and includes the use of deep kernels with features learnt using unsupervised models such as auto-encoders. We highlight the applicability of our MMD-Fuse tests on both synthetic low-dimensional and real-world high-dimensional data, and compare its performance in terms of power against current state-of-the-art kernel tests.

Constructing a similarity graph from a set $X$ of data points in $ \mathbb{R}^d$ is the first step of many modern clustering algorithms. However, typical constructions of a similarity graph have high time complexity, and a quadratic space dependency with respect to $|X|$. We address this limitation and present a new algorithmic framework that constructs a sparse approximation of the fully connected similarity graph while preserving its cluster structure. Our presented algorithm is based on the kernel density estimation problem, and is applicable for arbitrary kernel functions. We compare our designed algorithm with the well-known implementations from the scikit-learn library and the FAISS library, and find that our method significantly outperforms the implementation from both libraries on a variety of datasets.

Recent research has developed several Monte Carlo methods for estimating the normalization constant (partition function) based on the idea of annealing. This means sampling successively from a path of distributions which interpolate between a tractable "proposal" distribution and the unnormalized "target" distribution. Prominent estimators in this family include annealed importance sampling and annealed noise-contrastive estimation (NCE). Such methods hinge on a number of design choices: which estimator to use, which path of distributions to use and whether to use a path at all; so far, there is no definitive theory on which choices are efficient. Here, we evaluate each design choice by the asymptotic estimation error it produces. First, we show that using NCE is more efficient than the importance sampling estimator, but in the limit of infinitesimal path steps, the difference vanishes. Second, we find that using the geometric path brings down the estimation error from an exponential to a polynomial function of the parameter distance between the target and proposal distributions. Third, we find that the arithmetic path, while rarely used, can offer optimality properties over the universally-used geometric path. In fact, in a particular limit, the optimal path is arithmetic. Based on this theory, we finally propose a two-step estimator to approximate the optimal path in an efficient way.

Influence functions (IF) have been seen as a technique for explaining model predictions through the lens of the training data. Their utility is assumed to be in identifying training examples "responsible" for a prediction so that, for example, correcting a prediction is possible by intervening on those examples (removing or editing them) and retraining the model. However, recent empirical studies have shown that the existing methods of estimating IF predict the leave-one-out-and-retrain effect poorly. In order to understand the mismatch between the theoretical promise and the practical results, we analyse five assumptions made by IF methods which are problematic for modern-scale deep neural networks and which concern convexity, numeric stability, training trajectory and parameter divergence. This allows us to clarify what can be expected theoretically from IF. We show that while most assumptions can be addressed successfully, the parameter divergence poses a clear limitation on the predictive power of IF: influence fades over training time even with deterministic training. We illustrate this theoretical result with BERT and ResNet models. Another conclusion from the theoretical analysis is that IF are still useful for model debugging and correcting even though some of the assumptions made in prior work do not hold: using natural language processing and computer vision tasks, we verify that mis-predictions can be successfully corrected by taking only a few fine-tuning steps on influential examples.

Intelligent agents use internal world models to reason and make predictions about different courses of their actions at many scales. Devising learning paradigms and architectures that allow machines to learn world models that operate at multiple levels of temporal abstractions while dealing with complex uncertainty predictions is a major technical hurdle. In this work, we propose a probabilistic formalism to learn multi-time scale world models which we call the Multi Time Scale State Space (MTS3) model. Our model uses a computationally efficient inference scheme on multiple time scales for highly accurate long-horizon predictions and uncertainty estimates over several seconds into the future. Our experiments, which focus on action conditional long horizon future predictions, show that MTS3 outperforms recent methods on several system identification benchmarks including complex simulated and real-world dynamical systems.

Recent advances in neuroscientific experimental techniques have enabled us to simultaneously record the activity of thousands of neurons across multiple brain regions. This has led to a growing need for computational tools capable of analyzing how task-relevant information is represented and communicated between several brain regions. Partial information decompositions (PIDs) have emerged as one such tool, quantifying how much unique, redundant and synergistic information two or more brain regions carry about a task-relevant message. However, computing PIDs is computationally challenging in practice, and statistical issues such as the bias and variance of estimates remain largely unexplored. In this paper, we propose a new method for efficiently computing and estimating a PID definition on multivariate Gaussian distributions. We show empirically that our method satisfies an intuitive additivity property, and recovers the ground truth in a battery of canonical examples, even at high dimensionality. We also propose and evaluate, for the first time, a method to correct the bias in PID estimates at finite sample sizes. Finally, we demonstrate that our Gaussian PID effectively characterizes inter-areal interactions in the mouse brain, revealing higher redundancy between visual areas when a stimulus is behaviorally relevant.

Recurrent neural networks (RNNs) are popular machine learning tools for modeling and forecasting sequential data and for inferring dynamical systems (DS) from observed time series. Concepts from DS theory (DST) have variously been used to further our understanding of both, how trained RNNs solve complex tasks, and the training process itself. Bifurcations are particularly important phenomena in DS, including RNNs, that refer to topological (qualitative) changes in a system's dynamical behavior as one or more of its parameters are varied. Knowing the bifurcation structure of an RNN will thus allow to deduce many of its computational and dynamical properties, like its sensitivity to parameter variations or its behavior during training. In particular, bifurcations may account for sudden loss jumps observed in RNN training that could severely impede the training process. Here we first mathematically prove for a particular class of ReLU-based RNNs that certain bifurcations are indeed associated with loss gradients tending toward infinity or zero. We then introduce a novel heuristic algorithm for detecting all fixed points and $k$-cycles in ReLU-based RNNs and their existence and stability regions, hence bifurcation manifolds in parameter space. In contrast to previous numerical algorithms for finding fixed points and common continuation methods, our algorithm provides $\textit{exact}$ results and returns fixed points and cycles up to high orders with surprisingly good scaling behavior. We exemplify the algorithm on the analysis of the training process of RNNs, and find that the recently introduced technique of generalized teacher forcing completely avoids certain types of bifurcations in training. Thus, besides facilitating the DST analysis of trained RNNs, our algorithm provides a powerful instrument for analyzing the training process itself.

In various engineering and applied science applications, repetitive numerical simulations of partial differential equations (PDEs) for varying input parameters are often required (e.g., aircraft shape optimization over many design parameters) and solvers are required to perform rapid execution. In this study, we suggest a path that potentially opens up a possibility for physics-informed neural networks (PINNs), emerging deep-learning-based solvers, to be considered as one such solver. Although PINNs have pioneered a proper integration of deep-learning and scientific computing, they require repetitive time-consuming training of neural networks, which is not suitable for many-query scenarios. To address this issue, we propose a lightweight low-rank PINNs containing only hundreds of model parameters and an associated hypernetwork-based meta-learning algorithm, which allows efficient approximation of solutions of PDEs for varying ranges of PDE input parameters. Moreover, we show that the proposed method is effective in overcoming a challenging issue, known as "failure modes" of PINNs.

When deploying machine learning estimators in science and engineering (SAE) domains, it is critical to avoid failed estimations that can have disastrous consequences, e.g., in aero engine design. This work focuses on detecting and correcting failed state estimations before adopting them in SAE inverse problems, by utilizing simulations and performance metrics guided by physical laws. We suggest to flag a machine learning estimation when its physical model error exceeds a feasible threshold, and propose a novel approach, GEESE, to correct it through optimization, aiming at delivering both low error and high efficiency. The key designs of GEESE include (1) a hybrid surrogate error model to provide fast error estimations to reduce simulation cost and to enable gradient based backpropagation of error feedback, and (2) two generative models to approximate the probability distributions of the candidate states for simulating the exploitation and exploration behaviours. All three models are constructed as neural networks. GEESE is tested on three real-world SAE inverse problems and compared to a number of state-of-the-art optimization/search approaches. Results show that it fails the least number of times in terms of finding a feasible state correction, and requires physical evaluations less frequently in general.

We introduce a two-stage probabilistic framework for statistical downscaling using unpaired data. Statistical downscaling seeks a probabilistic map to transform low-resolution data from a biased coarse-grained numerical scheme to high-resolution data that is consistent with a high-fidelity scheme. Our framework tackles the problem by composing two transformations: (i) a debiasing step via an optimal transport map, and (ii) an upsampling step achieved by a probabilistic diffusion model with a posteriori conditional sampling. This approach characterizes a conditional distribution without needing paired data, and faithfully recovers relevant physical statistics from biased samples. We demonstrate the utility of the proposed approach on one- and two-dimensional fluid flow problems, which are representative of the core difficulties present in numerical simulations of weather and climate. Our method produces realistic high-resolution outputs from low-resolution inputs, by upsampling resolutions of $8\times$ and $16\times$. Moreover, our procedure correctly matches the statistics of physical quantities, even when the low-frequency content of the inputs and outputs do not match, a crucial but difficult-to-satisfy assumption needed by current state-of-the-art alternatives. Code for this work is available at: https://github.com/google-research/swirl-dynamics/tree/main/swirl_dynamics/projects/probabilistic_diffusion.

Score matching is an alternative to maximum likelihood (ML) for estimating a probability distribution parametrized up to a constant of proportionality. By fitting the ''score'' of the distribution, it sidesteps the need to compute this constant of proportionality (which is often intractable). While score matching and variants thereof are popular in practice, precise theoretical understanding of the benefits and tradeoffs with maximum likelihood---both computational and statistical---are not well understood. In this work, we give the first example of a natural exponential family of distributions such that the score matching loss is computationally efficient to optimize, and has a comparable statistical efficiency to ML, while the ML loss is intractable to optimize using a gradient-based method. The family consists of exponentials of polynomials of fixed degree, and our result can be viewed as a continuous analogue of recent developments in the discrete setting. Precisely, we show: (1) Designing a zeroth-order or first-order oracle for optimizing the maximum likelihood loss is NP-hard. (2) Maximum likelihood has a statistical efficiency polynomial in the ambient dimension and the radius of the parameters of the family. (3) Minimizing the score matching loss is both computationally and statistically efficient, with complexity polynomial in the ambient dimension.

Accurate prediction of dynamical systems in unstructured meshes has recently shown successes in scientific simulations. Many dynamical systems have a nonnegligible level of stochasticity introduced by various factors (e.g. chaoticity), so there is a need for a unified framework that captures both deterministic and stochastic components in the rollouts of these systems. Inspired by regeneration learning, we propose a new model that combines generative and sequential networks to model dynamical systems. Specifically, we use an autoencoder to learn compact representations of full-space physical variables in a low-dimensional space. We then integrate a transformer with a conditional normalizing flow model to model the temporal sequence of latent representations. We evaluate the new model in both deterministic and stochastic systems. The model outperforms several competitive baseline models and makes more accurate predictions of deterministic systems. Its own prediction error is also reflected in its uncertainty estimations. When predicting stochastic systems, the proposed model generates high-quality rollout samples. The mean and variance of these samples well match the statistics of samples computed from expensive numerical simulations.

We consider the problem of learning the exact skeleton of general discrete Bayesian networks from potentially corrupted data. Building on distributionally robust optimization and a regression approach, we propose to optimize the most adverse risk over a family of distributions within bounded Wasserstein distance or KL divergence to the empirical distribution. The worst-case risk accounts for the effect of outliers. The proposed approach applies for general categorical random variables without assuming faithfulness, an ordinal relationship or a specific form of conditional distribution. We present efficient algorithms and show the proposed methods are closely related to the standard regularized regression approach. Under mild assumptions, we derive non-asymptotic guarantees for successful structure learning with logarithmic sample complexities for bounded-degree graphs. Numerical study on synthetic and real datasets validates the effectiveness of our method.

This paper presents new quadrature rules for functions in a reproducing kernel Hilbert space using nodes drawn by a sampling algorithm known as randomly pivoted Cholesky. The resulting computational procedure compares favorably to previous kernel quadrature methods, which either achieve low accuracy or require solving a computationally challenging sampling problem. Theoretical and numerical results show that randomly pivoted Cholesky is fast and achieves comparable quadrature error rates to more computationally expensive quadrature schemes based on continuous volume sampling, thinning, and recombination. Randomly pivoted Cholesky is easily adapted to complicated geometries with arbitrary kernels, unlocking new potential for kernel quadrature.

Two-photon optogenetics has transformed our ability to probe the structure and function of neural circuits. However, achieving precise optogenetic control of neural ensemble activity has remained fundamentally constrained by the problem of off-target stimulation (OTS): the inadvertent activation of nearby non-target neurons due to imperfect confinement of light onto target neurons. Here we propose a novel computational approach to this problem called Bayesian target optimisation. Our approach uses nonparametric Bayesian inference to model neural responses to optogenetic stimulation, and then optimises the laser powers and optical target locations needed to achieve a desired activity pattern with minimal OTS. We validate our approach in simulations and using data from in vitro experiments, showing that Bayesian target optimisation considerably reduces OTS across all conditions we test. Together, these results establish our ability to overcome OTS, enabling optogenetic stimulation with substantially improved precision.

The causal revolution has stimulated interest in understanding complex relationships in various fields. Most of the existing methods aim to discover causal relationships among all variables within a complex large-scale graph. However, in practice, only a small subset of variables in the graph are relevant to the outcomes of interest. Consequently, causal estimation with the full causal graph---particularly given limited data---could lead to numerous *falsely discovered, spurious* variables that exhibit high correlation with, but exert no causal impact on, the target outcome. In this paper, we propose learning a class of *necessary and sufficient causal graphs (NSCG)* that exclusively comprises causally relevant variables for an outcome of interest, which we term *causal features*. The key idea is to employ *probabilities of causation* to systematically evaluate the importance of features in the causal graph, allowing us to identify a subgraph relevant to the outcome of interest. To learn NSCG from data, we develop a *necessary and sufficient causal structural learning (NSCSL)* algorithm, by establishing theoretical properties and relationships between probabilities of causation and natural causal effects of features. Across empirical studies of simulated and real data, we demonstrate that NSCSL outperforms existing algorithms and can reveal crucial yeast genes for target heritable traits of interest.

Learning to control unknown nonlinear dynamical systems is a fundamental problem in reinforcement learning and control theory. A commonly applied approach is to first explore the environment (exploration), learn an accurate model of it (system identification), and then compute an optimal controller with the minimum cost on this estimated system (policy optimization). While existing work has shown that it is possible to learn a uniformly good model of the system (Mania et al., 2020), in practice, if we aim to learn a good controller with a low cost on the actual system, certain system parameters may be significantly more critical than others, and we therefore ought to focus our exploration on learning such parameters. In this work, we consider the setting of nonlinear dynamical systems and seek to formally quantify, in such settings, (a) which parameters are most relevant to learning a good controller, and (b) how we can best explore so as to minimize uncertainty in such parameters. Inspired by recent work in linear systems (Wagenmaker et al., 2021), we show that minimizing the controller loss in nonlinear systems translates to estimating the system parameters in a particular, task-dependent metric. Motivated by this, we develop an algorithm able to efficiently explore the system to reduce uncertainty in this metric, and prove a lower bound showing that our approach learns a controller at a near-instance-optimal rate. Our algorithm relies on a general reduction from policy optimization to optimal experiment design in arbitrary systems, and may be of independent interest. We conclude with experiments demonstrating the effectiveness of our method in realistic nonlinear robotic systems.

Coupling normalizing flows allow for fast sampling and density evaluation, making them the tool of choice for probabilistic modeling of physical systems. However, the standard coupling architecture precludes endowing flows that operate on the Cartesian coordinates of atoms with the SE(3) and permutation invariances of physical systems. This work proposes a coupling flow that preserves SE(3) and permutation equivariance by performing coordinate splits along additional augmented dimensions. At each layer, the flow maps atoms' positions into learned SE(3) invariant bases, where we apply standard flow transformations, such as monotonic rational-quadratic splines, before returning to the original basis. Crucially, our flow preserves fast sampling and density evaluation, and may be used to produce unbiased estimates of expectations with respect to the target distribution via importance sampling. When trained on the DW4, LJ13, and QM9-positional datasets, our flow is competitive with equivariant continuous normalizing flows, while allowing sampling more than an order of magnitude faster. Moreover, to the best of our knowledge, we are the first to learn the full Boltzmann distribution of alanine dipeptide by only modeling the Cartesian positions of its atoms. Lastly, we demonstrate that our flow can be trained to approximately sample from the Boltzmann distribution of the DW4 and LJ13 particle systems using only their energy functions.

We present a novel approach to non-convex optimization with certificates, which handles smooth functions on the hypercube or on the torus. Unlike traditional methods that rely on algebraic properties, our algorithm exploits the regularity of the target function intrinsic in the decay of its Fourier spectrum. By defining a tractable family of models, we allow {\em at the same time} to obtain precise certificates and to leverage the advanced and powerful computational techniques developed to optimize neural networks. In this way the scalability of our approach is naturally enhanced by parallel computing with GPUs. Our approach, when applied to the case of polynomials of moderate dimensions but with thousands of coefficients, outperforms the state-of-the-art optimization methods with certificates, as the ones based on Lasserre's hierarchy, addressing problems intractable for the competitors.

Gaussian processes are used in many machine learning applications that rely on uncertainty quantification. Recently, computational tools for working with these models in geometric settings, such as when inputs lie on a Riemannian manifold, have been developed. This raises the question: can these intrinsic models be shown theoretically to lead to better performance, compared to simply embedding all relevant quantities into $\mathbb{R}^d$ and using the restriction of an ordinary Euclidean Gaussian process? To study this, we prove optimal contraction rates for intrinsic Matérn Gaussian processes defined on compact Riemannian manifolds. We also prove analogous rates for extrinsic processes using trace and extension theorems between manifold and ambient Sobolev spaces: somewhat surprisingly, the rates obtained turn out to coincide with those of the intrinsic processes, provided that their smoothness parameters are matched appropriately. We illustrate these rates empirically on a number of examples, which, mirroring prior work, show that intrinsic processes can achieve better performance in practice. Therefore, our work shows that finer-grained analyses are needed to distinguish between different levels of data-efficiency of geometric Gaussian processes, particularly in settings which involve small data set sizes and non-asymptotic behavior.

We introduce a general framework for active learning in regression problems. Our framework extends the standard setup by allowing for general types of data, rather than merely pointwise samples of the target function. This generalization covers many cases of practical interest, such as data acquired in transform domains (e.g., Fourier data), vector-valued data (e.g., gradient-augmented data), data acquired along continuous curves, and, multimodal data (i.e., combinations of different types of measurements). Our framework considers random sampling according to a finite number of sampling measures and arbitrary nonlinear approximation spaces (model classes). We introduce the concept of \textit{generalized Christoffel functions} and show how these can be used to optimize the sampling measures. We prove that this leads to near-optimal sample complexity in various important cases. This paper focuses on applications in scientific computing, where active learning is often desirable, since it is usually expensive to generate data. We demonstrate the efficacy of our framework for gradient-augmented learning with polynomials, Magnetic Resonance Imaging (MRI) using generative models and adaptive sampling for solving PDEs using Physics-Informed Neural Networks (PINNs).

We propose Tree Variational Autoencoder (TreeVAE), a new generative hierarchical clustering model that learns a flexible tree-based posterior distribution over latent variables. TreeVAE hierarchically divides samples according to their intrinsic characteristics, shedding light on hidden structures in the data. It adapts its architecture to discover the optimal tree for encoding dependencies between latent variables. The proposed tree-based generative architecture enables lightweight conditional inference and improves generative performance by utilizing specialized leaf decoders. We show that TreeVAE uncovers underlying clusters in the data and finds meaningful hierarchical relations between the different groups on a variety of datasets, including real-world imaging data. We present empirically that TreeVAE provides a more competitive log-likelihood lower bound than the sequential counterparts. Finally, due to its generative nature, TreeVAE is able to generate new samples from the discovered clusters via conditional sampling.

We provide practical, efficient, and nonparametric methods for auditing the fairness of deployed classification and regression models. Whereas previous work relies on a fixed-sample size, our methods are sequential and allow for the continuous monitoring of incoming data, making them highly amenable to tracking the fairness of real-world systems. We also allow the data to be collected by a probabilistic policy as opposed to sampled uniformly from the population. This enables auditing to be conducted on data gathered for another purpose. Moreover, this policy may change over time and different policies may be used on different subpopulations. Finally, our methods can handle distribution shift resulting from either changes to the model or changes in the underlying population. Our approach is based on recent progress in anytime-valid inference and game-theoretic statistics---the ``testing by betting'' framework in particular. These connections ensure that our methods are interpretable, fast, and easy to implement. We demonstrate the efficacy of our approach on three benchmark fairness datasets.

Denoising diffusion models are a powerful type of generative models used to capture complex distributions of real-world signals. However, their applicability is limited to scenarios where training samples are readily available, which is not always the case in real-world applications. For example, in inverse graphics, the goal is to generate samples from a distribution of 3D scenes that align with a given image, but ground-truth 3D scenes are unavailable and only 2D images are accessible. To address this limitation, we propose a novel class of denoising diffusion probabilistic models that learn to sample from distributions of signals that are never directly observed. Instead, these signals are measured indirectly through a known differentiable forward model, which produces partial observations of the unknown signal. Our approach involves integrating the forward model directly into the denoising process. A key contribution of our work is the integration of a differentiable forward model into the denoising process. This integration effectively connects the generative modeling of observations with the generative modeling of the underlying signals, allowing for end-to-end training of a conditional generative model over signals. During inference, our approach enables sampling from the distribution of underlying signals that are consistent with a given partial observation. We demonstrate the effectiveness of our method on three challenging computer vision tasks. For instance, in the context of inverse graphics, our model enables direct sampling from the distribution of 3D scenes that align with a single 2D input image.

Since their initial introduction, score-based diffusion models (SDMs) have been successfully applied to solve a variety of linear inverse problems in finite-dimensional vector spaces due to their ability to efficiently approximate the posterior distribution. However, using SDMs for inverse problems in infinite-dimensional function spaces has only been addressed recently, primarily through methods that learn the unconditional score. While this approach is advantageous for some inverse problems, it is mostly heuristic and involves numerous computationally costly forward operator evaluations during posterior sampling. To address these limitations, we propose a theoretically grounded method for sampling from the posterior of infinite-dimensional Bayesian linear inverse problems based on amortized conditional SDMs. In particular, we prove that one of the most successful approaches for estimating the conditional score in finite dimensions—the conditional denoising estimator—can also be applied in infinite dimensions. A significant part of our analysis is dedicated to demonstrating that extending infinite-dimensional SDMs to the conditional setting requires careful consideration, as the conditional score typically blows up for small times, contrarily to the unconditional score. We conclude by presenting stylized and large-scale numerical examples that validate our approach, offer additional insights, and demonstrate that our method enables large-scale, discretization-invariant Bayesian inference.

Stein discrepancies have emerged as a powerful tool for retrospective improvement of Markov chain Monte Carlo output. However, the question of how to design Markov chains that are well-suited to such post-processing has yet to be addressed. This paper studies Stein importance sampling, in which weights are assigned to the states visited by a $\Pi$-invariant Markov chain to obtain a consistent approximation of $P$, the intended target. Surprisingly, the optimal choice of $\Pi$ is not identical to the target $P$; we therefore propose an explicit construction for $\Pi$ based on a novel variational argument. Explicit conditions for convergence of Stein $\Pi$-Importance Sampling are established. For $\approx 70$% of tasks in the PosteriorDB benchmark, a significant improvement over the analogous post-processing of $P$-invariant Markov chains is reported.

Time-dependent partial differential equations (PDEs) are ubiquitous in science and engineering. Recently, mostly due to the high computational cost of traditional solution techniques, deep neural network based surrogates have gained increased interest. The practical utility of such neural PDE solvers relies on their ability to provide accurate, stable predictions over long time horizons, which is a notoriously hard problem. In this work, we present a large-scale analysis of common temporal rollout strategies, identifying the neglect of non-dominant spatial frequency information, often associated with high frequencies in PDE solutions, as the primary pitfall limiting stable, accurate rollout performance. Based on these insights, we draw inspiration from recent advances in diffusion models to introduce PDE-Refiner; a novel model class that enables more accurate modeling of all frequency components via a multistep refinement process. We validate PDE-Refiner on challenging benchmarks of complex fluid dynamics, demonstrating stable and accurate rollouts that consistently outperform state-of-the-art models, including neural, numerical, and hybrid neural-numerical architectures. We further demonstrate that PDE-Refiner greatly enhances data efficiency, since the denoising objective implicitly induces a novel form of spectral data augmentation. Finally, PDE-Refiner's connection to diffusion models enables an accurate and efficient assessment of the model's predictive uncertainty, allowing us to estimate when the surrogate becomes inaccurate.

Counterfactual inference aims to answer retrospective "what if" questions and thus belongs to the most fine-grained type of inference in Pearl's causality ladder. Existing methods for counterfactual inference with continuous outcomes aim at point identification and thus make strong and unnatural assumptions about the underlying structural causal model. In this paper, we relax these assumptions and aim at partial counterfactual identification of continuous outcomes, i.e., when the counterfactual query resides in an ignorance interval with informative bounds. We prove that, in general, the ignorance interval of the counterfactual queries has non-informative bounds, already when functions of structural causal models are continuously differentiable. As a remedy, we propose a novel sensitivity model called Curvature Sensitivity Model. This allows us to obtain informative bounds by bounding the curvature of level sets of the functions. We further show that existing point counterfactual identification methods are special cases of our Curvature Sensitivity Model when the bound of the curvature is set to zero. We then propose an implementation of our Curvature Sensitivity Model in the form of a novel deep generative model, which we call Augmented Pseudo-Invertible Decoder. Our implementation employs (i) residual normalizing flows with (ii) variational augmentations. We empirically demonstrate the effectiveness of our Augmented Pseudo-Invertible Decoder. To the best of our knowledge, ours is the first partial identification model for Markovian structural causal models with continuous outcomes.

Graph neural networks (GNNs) are vulnerable to adversarial perturbations, including those that affect both node features and graph topology. This paper investigates GNNs derived from diverse neural flows, concentrating on their connection to various stability notions such as BIBO stability, Lyapunov stability, structural stability, and conservative stability. We argue that Lyapunov stability, despite its common use, does not necessarily ensure adversarial robustness. Inspired by physics principles, we advocate for the use of conservative Hamiltonian neural flows to construct GNNs that are robust to adversarial attacks. The adversarial robustness of different neural flow GNNs is empirically compared on several benchmark datasets under a variety of adversarial attacks. Extensive numerical experiments demonstrate that GNNs leveraging conservative Hamiltonian flows with Lyapunov stability substantially improve robustness against adversarial perturbations. The implementation code of experiments is available at \url{https://github.com/zknus/NeurIPS-2023-HANG-Robustness}.

We consider the problem of estimating the causal effect of a treatment on an outcome in linear structural causal models (SCM) with latent confounders when we have access to a single proxy variable. Several methods (such as difference-in-difference (DiD) estimator or negative outcome control) have been proposed in this setting in the literature. However, these approaches require either restrictive assumptions on the data generating model or having access to at least two proxy variables. We propose a method to estimate the causal effect using cross moments between the treatment, the outcome, and the proxy variable. In particular, we show that the causal effect can be identified with simple arithmetic operations on the cross moments if the latent confounder in linear SCM is non-Gaussian. In this setting, DiD estimator provides an unbiased estimate only in the special case where the latent confounder has exactly the same direct causal effects on the outcomes in the pre-treatment and post-treatment phases. This translates to the common trend assumption in DiD, which we effectively relax. Additionally, we provide an impossibility result that shows the causal effect cannot be identified if the observational distribution over the treatment, the outcome, and the proxy is jointly Gaussian. Our experiments on both synthetic and real-world datasets showcase the effectiveness of the proposed approach in estimating the causal effect.

Gromov-Wasserstein (GW) distance is a powerful tool for comparing and aligning probability distributions supported on different metric spaces. Recently, GW has become the main modeling technique for aligning heterogeneous data for a wide range of graph learning tasks. However, the GW distance is known to be highly sensitive to outliers, which can result in large inaccuracies if the outliers are given the same weight as other samples in the objective function. To mitigate this issue, we introduce a new and robust version of the GW distance called RGW. RGW features optimistically perturbed marginal constraints within a Kullback-Leibler divergence-based ambiguity set. To make the benefits of RGW more accessible in practice, we develop a computationally efficient and theoretically provable procedure using Bregman proximal alternating linearized minimization algorithm. Through extensive experimentation, we validate our theoretical results and demonstrate the effectiveness of RGW on real-world graph learning tasks, such as subgraph matching and partial shape correspondence.

Non-linear dynamical systems can be handily described by the associated Koopman operator, whose action evolves every observable of the system forward in time. Learning the Koopman operator and its spectral decomposition from data is enabled by a number of algorithms. In this work we present for the first time non-asymptotic learning bounds for the Koopman eigenvalues and eigenfunctions. We focus on time-reversal-invariant stochastic dynamical systems, including the important example of Langevin dynamics. We analyze two popular estimators: Extended Dynamic Mode Decomposition (EDMD) and Reduced Rank Regression (RRR). Our results critically hinge on novel {minimax} estimation bounds for the operator norm error, that may be of independent interest. Our spectral learning bounds are driven by the simultaneous control of the operator norm error and a novel metric distortion functional of the estimated eigenfunctions. The bounds indicates that both EDMD and RRR have similar variance, but EDMD suffers from a larger bias which might be detrimental to its learning rate. Our results shed new light on the emergence of spurious eigenvalues, an issue which is well known empirically. Numerical experiments illustrate the implications of the bounds in practice.

Non-convex sampling is a key challenge in machine learning, central to non-convex optimization in deep learning as well as to approximate probabilistic inference. Despite its significance, theoretically there remain some important challenges: Existing guarantees suffer from the drawback of lacking guarantees for the last-iterates, and little is known beyond the elementary schemes of stochastic gradient Langevin dynamics. To address these issues, we develop a novel framework that lifts the above issues by harnessing several tools from the theory of dynamical systems. Our key result is that, for a large class of state-of-the-art sampling schemes, their last-iterate convergence in Wasserstein distances can be reduced to the study of their continuous-time counterparts, which is much better understood. Coupled with standard assumptions of MCMC sampling, our theory immediately yields the last-iterate Wasserstein convergence of many advanced sampling schemes such as mirror Langevin, proximal, randomized mid-point, and Runge-Kutta methods.

Multi-marginal Optimal Transport (mOT), a generalization of OT, aims at minimizing the integral of a cost function with respect to a distribution with some prescribed marginals. In this paper, we consider an entropic version of mOT with a tree-structured quadratic cost, i.e., a function that can be written as a sum of pairwise cost functions between the nodes of a tree. To address this problem, we develop Tree-based Diffusion Schr\"odinger Bridge (TreeDSB), an extension of the Diffusion Schr\"odinger Bridge (DSB) algorithm. TreeDSB corresponds to a dynamic and continuous state-space counterpart of the multimarginal Sinkhorn algorithm. A notable use case of our methodology is to compute Wasserstein barycenters which can be recast as the solution of a mOT problem on a star-shaped tree. We demonstrate that our methodology can be applied in high-dimensional settings such as image interpolation and Bayesian fusion.

Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic features which would require domain expertise and may suffer from limited approximation capability. In this paper, we propose a deep autoregressive model for phylogenetic inference based on graph neural networks (GNNs), called ARTree. By decomposing a tree topology into a sequence of leaf node addition operations and modeling the involved conditional distributions based on learnable topological features via GNNs, ARTree can provide a rich family of distributions over tree topologies that have simple sampling algorithms, without using heuristic features. We demonstrate the effectiveness and efficiency of our method on a benchmark of challenging real data tree topology density estimation and variational Bayesian phylogenetic inference problems.

Reasoning system dynamics is one of the most important analytical approaches for many scientific studies. With the initial state of a system as input, the recent graph neural networks (GNNs)-based methods are capable of predicting the future state distant in time with high accuracy. Although these methods have diverse designs in modeling the coordinates and interacting forces of the system, we show that they actually share a common paradigm that learns the integration of the velocity over the interval between the initial and terminal coordinates. However, their integrand is constant w.r.t. time. Inspired by this observation, we propose a new approach to predict the integration based on several velocity estimations with Newton–Cotes formulas and prove its effectiveness theoretically. Extensive experiments on several benchmarks empirically demonstrate consistent and significant improvement compared with the state-of-the-art methods.

Continuous-time score-based generative models consist of a pair of stochastic differential equations (SDEs)—a forward SDE that smoothly transitions data into a noise space and a reverse SDE that incrementally eliminates noise from a Gaussian prior distribution to generate data distribution samples—are intrinsically connected by the time-reversal theory on diffusion processes. In this paper, we investigate the use of stochastic evolution equations in Hilbert spaces, which expand the applicability of SDEs in two aspects: sample space and evolution operator, so they enable encompassing recent variations of diffusion models, such as generating functional data or replacing drift coefficients with image transformation. To this end, we derive a generalized time-reversal formula to build a bridge between probabilistic diffusion models and stochastic evolution equations and propose a score-based generative model called Hilbert Diffusion Model (HDM). Combining with Fourier neural operator, we verify the superiority of HDM for sampling functions from functional datasets with a power of kernel two-sample test of 4.2 on Quadratic, 0.2 on Melbourne, and 3.6 on Gridwatch, which outperforms existing diffusion models formulated in function spaces. Furthermore, the proposed method shows its strength in motion synthesis tasks by utilizing the Wiener process with values in Hilbert space. Finally, our empirical results on image datasets also validate a connection between HDM and diffusion models using heat dissipation, revealing the potential for exploring evolution operators and sample spaces.

The goal of causal representation learning is to find a representation of data that consists of causally related latent variables. We consider a setup where one has access to data from multiple domains that potentially share a causal representation. Crucially, observations in different domains are assumed to be unpaired, that is, we only observe the marginal distribution in each domain but not their joint distribution. In this paper, we give sufficient conditions for identifiability of the joint distribution and the shared causal graph in a linear setup. Identifiability holds if we can uniquely recover the joint distribution and the shared causal representation from the marginal distributions in each domain. We transform our results into a practical method to recover the shared latent causal graph.

Many common types of data can be represented as functions that map coordinates to signal values, such as pixel locations to RGB values in the case of an image. Based on this view, data can be compressed by overfitting a compact neural network to its functional representation and then encoding the network weights. However, most current solutions for this are inefficient, as quantization to low-bit precision substantially degrades the reconstruction quality. To address this issue, we propose overfitting variational Bayesian neural networks to the data and compressing an approximate posterior weight sample using relative entropy coding instead of quantizing and entropy coding it. This strategy enables direct optimization of the rate-distortion performance by minimizing the $\beta$-ELBO, and target different rate-distortion trade-offs for a given network architecture by adjusting $\beta$. Moreover, we introduce an iterative algorithm for learning prior weight distributions and employ a progressive refinement process for the variational posterior that significantly enhances performance. Experiments show that our method achieves strong performance on image and audio compression while retaining simplicity.

Wasserstein distance (WD) and the associated optimal transport plan have been proven useful in many applications where probability measures are at stake. In this paper, we propose a new proxy of the squared WD, coined $\textnormal{min-SWGG}$, that is based on the transport map induced by an optimal one-dimensional projection of the two input distributions. We draw connections between $\textnormal{min-SWGG}$, and Wasserstein generalized geodesics in which the pivot measure is supported on a line. We notably provide a new closed form for the exact Wasserstein distance in the particular case of one of the distributions supported on a line allowing us to derive a fast computational scheme that is amenable to gradient descent optimization. We show that $\textnormal{min-SWGG}$, is an upper bound of WD and that it has a complexity similar to as Sliced-Wasserstein, with the additional feature of providing an associated transport plan. We also investigate some theoretical properties such as metricity, weak convergence, computational and topological properties. Empirical evidences support the benefits of $\textnormal{min-SWGG}$, in various contexts, from gradient flows, shape matching and image colorization, among others.

Decision trees have gained popularity as interpretable surrogate models for learning-based control policies. However, providing safety guarantees for systems controlled by decision trees is an open challenge. We show that the problem is undecidable even for systems with the simplest dynamics, and PSPACE-complete for finite-horizon properties. The latter can be verified for discrete-time systems via bounded model checking. However, for continuous-time systems, such an approach requires discretization, thereby weakening the guarantees for the original system. This paper presents the first algorithm to directly verify decision-tree controlled system in continuous time. The key aspect of our method is exploiting the decision-tree structure to propagate a set-based approximation through the decision nodes. We demonstrate the effectiveness of our approach by verifying safety of several decision trees distilled to imitate neural-network policies for nonlinear systems.

Flexible models for probability distributions are an essential ingredient in many machine learning tasks. We develop and investigate a new class of probability distributions, which we call a Squared Neural Family (SNEFY), formed by squaring the 2-norm of a neural network and normalising it with respect to a base measure. Following the reasoning similar to the well established connections between infinitely wide neural networks and Gaussian processes, we show that SNEFYs admit closed form normalising constants in many cases of interest, thereby resulting in flexible yet fully tractable density models. SNEFYs strictly generalise classical exponential families, are closed under conditioning, and have tractable marginal distributions. Their utility is illustrated on a variety of density estimation, conditional density estimation, and density estimation with missing data tasks.

Decision trees are a well-established tool in machine learning for classification and regression tasks. In this paper, we introduce a novel non-parametric Bayesian model that uses variational inference to approximate a posterior distribution over the space of stochastic decision trees. We evaluate the model's performance on 18 datasets and demonstrate its competitiveness with other state-of-the-art methods in regression tasks. We also explore its application to causal inference problems. We provide a fully vectorized implementation of our algorithm in PyTorch.

Conditional independence (CI) testing is a fundamental and challenging task in modern statistics and machine learning. Many modern methods for CI testing rely on powerful supervised learning methods to learn regression functions or Bayes predictors as an intermediate step; we refer to this class of tests as regression-based tests. Although these methods are guaranteed to control Type-I error when the supervised learning methods accurately estimate the regression functions or Bayes predictors of interest, their behavior is less understood when they fail due to misspecified inductive biases; in other words, when the employed models are not flexible enough or when the training algorithm does not induce the desired predictors. Then, we study the performance of regression-based CI tests under misspecified inductive biases. Namely, we propose new approximations or upper bounds for the testing errors of three regression-based tests that depend on misspecification errors. Moreover, we introduce the Rao-Blackwellized Predictor Test (RBPT), a regression-based CI test robust against misspecified inductive biases. Finally, we conduct experiments with artificial and real data, showcasing the usefulness of our theory and methods.

Research in statistical learning has polarized into two general approaches to perform regression analysis: Transductive methods construct estimates directly based on exemplar data using generic relational principles which might suffer from the curse of dimensionality. Conversely, inductive methods can potentially fit highly complex functions at the cost of compute-intensive solution searches. In this work, we leverage the theory of vector-valued Reproducing Kernel Banach Spaces (RKBS) to propose a hybrid approach: We show that transductive regression systems can be meta-learned with gradient descent to form efficient _in-context_ neural approximators of function defined over both finite and infinite-dimensional spaces (operator regression). Once trained, our _Transducer_ can almost instantaneously capture new functional relationships and produce original image estimates, given a few pairs of input and output examples. We demonstrate the benefit of our meta-learned transductive approach to model physical systems influenced by varying external factors with little data at a fraction of the usual deep learning training costs for partial differential equations and climate modeling applications.

We address the problem of denoising data from a Gaussian mixture using a two-layer non-linear autoencoder with tied weights and a skip connection. We consider the high-dimensional limit where the number of training samples and the input dimension jointly tend to infinity while the number of hidden units remains bounded. We provide closed-form expressions for the denoising mean-squared test error. Building on this result, we quantitatively characterize the advantage of the considered architecture over the autoencoder without the skip connection that relates closely to principal component analysis. We further show that our results capture accurately the learning curves on a range of real datasets.

In $\mathbb{R}^d$, it is well-known that cumulants provide an alternative to moments that can achieve the same goals with numerous benefits such as lower variance estimators. In this paper we extend cumulants to reproducing kernel Hilbert spaces (RKHS) using tools from tensor algebras and show that they are computationally tractable by a kernel trick. These kernelized cumulants provide a new set of all-purpose statistics; the classical maximum mean discrepancy and Hilbert-Schmidt independence criterion arise as the degree one objects in our general construction. We argue both theoretically and empirically (on synthetic, environmental, and traffic data analysis) that going beyond degree one has several advantages and can be achieved with the same computational complexity and minimal overhead in our experiments.

Combinatorial optimization (CO) problems are often NP-hard and thus out of reach for exact algorithms, making them a tempting domain to apply machine learning methods. The highly structured constraints in these problems can hinder either optimization or sampling directly in the solution space. On the other hand, GFlowNets have recently emerged as a powerful machinery to efficiently sample from composite unnormalized densities sequentially and have the potential to amortize such solution-searching processes in CO, as well as generate diverse solution candidates. In this paper, we design Markov decision processes (MDPs) for different combinatorial problems and propose to train conditional GFlowNets to sample from the solution space. Efficient training techniques are also developed to benefit long-range credit assignment. Through extensive experiments on a variety of different CO tasks with synthetic and realistic data, we demonstrate that GFlowNet policies can efficiently find high-quality solutions. Our implementation is open-sourced at https://github.com/zdhNarsil/GFlowNet-CombOpt.

Stein Variational Gradient Descent (SVGD) is a popular particle-based variational inference algorithm with impressive empirical performance across various domains. Although the population (i.e, infinite-particle) limit dynamics of SVGD is well characterized, its behavior in the finite-particle regime is far less understood. To this end, our work introduces the notion of *virtual particles* to develop novel stochastic approximations of population-limit SVGD dynamics in the space of probability measures, that are exactly realizable using finite particles. As a result, we design two computationally efficient variants of SVGD, namely VP-SVGD and GB-SVGD, with provably fast finite-particle convergence rates. Our algorithms can be viewed as specific random-batch approximations of SVGD, which are computationally more efficient than ordinary SVGD. We show that the $n$ particles output by VP-SVGD and GB-SVGD, run for $T$ steps with batch-size $K$, are at-least as good as i.i.d samples from a distribution whose Kernel Stein Discrepancy to the target is at most $O(\tfrac{d^{1/3}}{(KT)^{1/6}})$ under standard assumptions. Our results also hold under a mild growth condition on the potential function, which is much weaker than the isoperimetric (e.g. Poincare Inequality) or information-transport conditions (e.g. Talagrand's Inequality $\mathsf{T}_1$) generally considered in prior works. As a corollary, we analyze the convergence of the empirical measure (of the particles output by VP-SVGD and GB-SVGD) to the target distribution and demonstrate a **double exponential improvement** over the best known finite-particle analysis of SVGD. Beyond this, our results present the **first known oracle complexities for this setting with polynomial dimension dependence**, thereby completely eliminating the curse of dimensionality exhibited by previously known finite-particle rates.

We propose a new class of generative model that naturally handles data of varying dimensionality by jointly modeling the state and dimension of each datapoint. The generative process is formulated as a jump diffusion process that makes jumps between different dimensional spaces. We first define a dimension destroying forward noising process, before deriving the dimension creating time-reversed generative process along with a novel evidence lower bound training objective for learning to approximate it. Simulating our learned approximation to the time-reversed generative process then provides an effective way of sampling data of varying dimensionality by jointly generating state values and dimensions. We demonstrate our approach on molecular and video datasets of varying dimensionality, reporting better compatibility with test-time diffusion guidance imputation tasks and improved interpolation capabilities versus fixed dimensional models that generate state values and dimensions separately.

We present a novel approach for explaining Gaussian processes (GPs) that can utilize the full analytical covariance structure present in GPs. Our method is based on the popular solution concept of Shapley values extended to stochastic cooperative games, resulting in explanations that are random variables. The GP explanations generated using our approach satisfy similar favorable axioms to standard Shapley values and possess a tractable covariance function across features and data observations. This covariance allows for quantifying explanation uncertainties and studying the statistical dependencies between explanations. We further extend our framework to the problem of predictive explanation, and propose a Shapley prior over the explanation function to predict Shapley values for new data based on previously computed ones. Our extensive illustrations demonstrate the effectiveness of the proposed approach.

*Molecular dynamics* (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds ($1\textrm{fs}=10^{-15}\textrm{s}$). MD is often used to compute equilibrium properties, which requires sampling from an equilibrium distribution such as the Boltzmann distribution. However, many important processes, such as binding and folding, occur over timescales of milliseconds or beyond, and cannot be efficiently sampled with conventional MD. Furthermore, new MD simulations need to be performed for each molecular system studied. We present *Timewarp*, an enhanced sampling method which uses a normalising flow as a proposal distribution in a Markov chain Monte Carlo method targeting the Boltzmann distribution. The flow is trained offline on MD trajectories and learns to make large steps in time, simulating the molecular dynamics of $10^{5} - 10^{6} \textrm{fs}$. Crucially, Timewarp is *transferable* between molecular systems: once trained, we show that it generalises to unseen small peptides (2-4 amino acids) at all-atom resolution, exploring their metastable states and providing wall-clock acceleration of sampling compared to standard MD. Our method constitutes an important step towards general, transferable algorithms for accelerating MD.

Since their inception, Variational Autoencoders (VAEs) have become central in machine learning. Despite their widespread use, numerous questions regarding their theoretical properties remain open. Using PAC-Bayesian theory, this work develops statistical guarantees for VAEs. First, we derive the first PAC-Bayesian bound for posterior distributions conditioned on individual samples from the data-generating distribution. Then, we utilize this result to develop generalization guarantees for the VAE's reconstruction loss, as well as upper bounds on the distance between the input and the regenerated distributions. More importantly, we provide upper bounds on the Wasserstein distance between the input distribution and the distribution defined by the VAE's generative model.

Model reparametrization, which follows the change-of-variable rule of calculus, is a popular way to improve the training of neural nets. But it can also be problematic since it can induce inconsistencies in, e.g., Hessian-based flatness measures, optimization trajectories, and modes of probability densities. This complicates downstream analyses: e.g. one cannot definitively relate flatness with generalization since arbitrary reparametrization changes their relationship. In this work, we study the invariance of neural nets under reparametrization from the perspective of Riemannian geometry. From this point of view, invariance is an inherent property of any neural net _if_ one explicitly represents the metric and uses the correct associated transformation rules. This is important since although the metric is always present, it is often implicitly assumed as identity, and thus dropped from the notation, then lost under reparametrization. We discuss implications for measuring the flatness of minima, optimization, and for probability-density maximization. Finally, we explore some interesting directions where invariance is useful.

Self-consistent Field (SCF) equation is a type of nonlinear eigenvalue problem in which the matrix to be eigen-decomposed is a function of its own eigenvectors. It is of great significance in computational science for its connection to the Schrödinger equation. Traditional fixed-point iteration methods for solving such equations suffer from non-convergence issues. In this work, we present a novel perspective on such SCF equations as a principal component analysis (PCA) for non-stationary time series, in which a distribution and its own top principal components are mutually updated over time, and the equilibrium state of the model corresponds to the solution of the SCF equations. By the new perspective, online PCA techniques are able to engage in so as to enhance the convergence of the model towards the equilibrium state, acting as a new set of tools for converging the SCF equations. With several numerical adaptations, we then develop a new algorithm for converging the SCF equation, and demonstrated its high convergence capacity with experiments on both synthesized and real electronic structure scenarios.

Measuring dependence between two random variables is of great importance in various domains but is difficult to compute in today's complex environments with high-dimensional data. Recently, slicing methods have shown to be a scalable approach to measuring mutual information (MI) between high-dimensional variables by projecting these variables into one-dimensional spaces. Unfortunately, these methods use uniform distributions of slicing directions, which generally discard informative features between variables and thus lead to inaccurate quantification of dependence. In this paper, we propose a principled framework that searches for an \textit{optimal} distribution of slices for MI. Importantly, we answer theoretical questions about finding the optimal slicing distribution in the context of MI and develop corresponding theoretical analyses. We also develop a practical algorithm, connecting our theoretical results with modern machine learning frameworks. Through comprehensive experiments in benchmark domains, we demonstrate significant gains in our information measure than state-of-the-art baselines.

Studying conditional independence among many variables with few observations is a challenging task. Gaussian Graphical Models (GGMs) tackle this problem by encouraging sparsity in the precision matrix through $l_q$ regularization with $q\leq1$. However, most GMMs rely on the $l_1$ norm because the objective is highly non-convex for sub-$l_1$ pseudo-norms. In the frequentist formulation, the $l_1$ norm relaxation provides the solution path as a function of the shrinkage parameter $\lambda$. In the Bayesian formulation, sparsity is instead encouraged through a Laplace prior, but posterior inference for different $\lambda$ requires repeated runs of expensive Gibbs samplers. Here we propose a general framework for variational inference with matrix-variate Normalizing Flow in GGMs, which unifies the benefits of frequentist and Bayesian frameworks. As a key improvement on previous work, we train with one flow a continuum of sparse regression models jointly for all regularization parameters $\lambda$ and all $l_q$ norms, including non-convex sub-$l_1$ pseudo-norms. Within one model we thus have access to (i) the evolution of the posterior for any $\lambda$ and any $l_q$ (pseudo-) norm, (ii) the marginal log-likelihood for model selection, and (iii) the frequentist solution paths through simulated annealing in the MAP limit.

Federated or multi-site studies have distinct advantages over single-site studies, including increased generalizability, the ability to study underrepresented populations, and the opportunity to study rare exposures and outcomes. However, these studies are complicated by the need to preserve the privacy of each individual's data, heterogeneity in their covariate distributions, and different data structures between sites. We propose a novel federated approach to derive valid causal inferences for a target population using multi-site data. We adjust for covariate shift and accommodate covariate mismatch between sites by developing a multiply-robust and privacy-preserving nuisance function estimation approach. Our methodology incorporates transfer learning to estimate ensemble weights to combine information from source sites. We show that these learned weights are efficient and optimal under different scenarios. We showcase the finite sample advantages of our approach in terms of efficiency and robustness compared to existing state-of-the-art approaches. We apply our approach to study the treatment effect of percutaneous coronary intervention (PCI) on the duration of hospitalization for patients experiencing acute myocardial infarction (AMI) with data from the Centers for Medicare \& Medicaid Services (CMS).

Solar power harbors immense potential in mitigating climate change by substantially reducing CO$_{2}$ emissions. Nonetheless, the inherent variability of solar irradiance poses a significant challenge for seamlessly integrating solar power into the electrical grid. While the majority of prior research has centered on employing purely time series-based methodologies for solar forecasting, only a limited number of studies have taken into account factors such as cloud cover or the surrounding physical context. In this paper, we put forth a deep learning architecture designed to harness spatio-temporal context using satellite data, to attain highly accurate day-ahead time-series forecasting for any given station, with a particular emphasis on forecasting Global Horizontal Irradiance (GHI). We also suggest a methodology to extract a distribution for each time step prediction, which can serve as a very valuable measure of uncertainty attached to the forecast. When evaluating models, we propose a testing scheme in which we separate particularly difficult examples from easy ones, in order to capture the model performances in crucial situations, which in the case of this study are the days suffering from varying cloudy conditions. Furthermore, we present a new multi-modal dataset gathering satellite imagery over a large zone and time series for solar irradiance and other related physical variables from multiple geographically diverse solar stations. Our approach exhibits robust performance in solar irradiance forecasting, including zero-shot generalization tests at unobserved solar stations, and holds great promise in promoting the effective integration of solar power into the grid.

The relationship between perception and inference, as postulated by Helmholtz in the 19th century, is paralleled in modern machine learning by generative models like Variational Autoencoders (VAEs) and their hierarchical variants. Here, we evaluate the role of hierarchical inference and its alignment with brain function in the domain of motion perception. We first introduce a novel synthetic data framework, Retinal Optic Flow Learning (ROFL), which enables control over motion statistics and their causes. We then present a new hierarchical VAE and test it against alternative models on two downstream tasks: (i) predicting ground truth causes of retinal optic flow (e.g., self-motion); and (ii) predicting the responses of neurons in the motion processing pathway of primates. We manipulate the model architectures (hierarchical versus non-hierarchical), loss functions, and the causal structure of the motion stimuli. We find that hierarchical latent structure in the model leads to several improvements. First, it improves the linear decodability of ground truth variables and does so in a sparse and disentangled manner. Second, our hierarchical VAE outperforms previous state-of-the-art models in predicting neuronal responses and exhibits sparse latent-to-neuron relationships. These results depend on the causal structure of the world, indicating that alignment between brains and artificial neural networks depends not only on architecture but also on matching ecologically relevant stimulus statistics. Taken together, our results suggest that hierarchical Bayesian inference underlines the brain's understanding of the world, and hierarchical VAEs can effectively model this understanding.

Combining test statistics from independent trials or experiments is a popular method of meta-analysis. However, there is very limited theoretical understanding of the power of the combined test, especially in high-dimensional models considering composite hypotheses tests. We derive a mathematical framework to study standard {meta-analysis} testing approaches in the context of the many normal means model, which serves as the platform to investigate more complex models. We introduce a natural and mild restriction on the meta-level combination functions of the local trials. This allows us to mathematically quantify the cost of compressing $m$ trials into real-valued test statistics and combining these. We then derive minimax lower and matching upper bounds for the separation rates of standard combination methods for e.g. p-values and e-values, quantifying the loss relative to using the full, pooled data. We observe an elbow effect, revealing that in certain cases combining the locally optimal tests in each trial results in a sub-optimal {meta-analysis} method and develop approaches to achieve the global optima. We also explore the possible gains of allowing limited coordination between the trial designs. Our results connect meta-analysis with bandwidth constraint distributed inference and build on recent information theoretic developments in the latter field.

Randomized experiments have been the gold standard for assessing the effectiveness of a treatment, policy, or intervention, spanning various fields, including social sciences, biomedical studies, and e-commerce. The classical complete randomization approach assigns treatments based on a pre-specified probability and may lead to inefficient use of data. Adaptive experiments improve upon complete randomization by sequentially learning and updating treatment assignment probabilities using accrued evidence during the experiment. Hence, they can help achieve efficient data use and higher estimation efficiency. However, their application can also raise fairness and equity concerns, as assignment probabilities may vary drastically across groups of participants. Furthermore, when treatment is expected to be extremely beneficial to certain groups of participants, it is more appropriate to expose many of these participants to favorable treatment. In response to these challenges, we propose a fair adaptive experiment strategy that simultaneously enhances data use efficiency, achieves an ``envy-free'' treatment assignment guarantee, and improves the overall welfare of participants. An important feature of our proposed strategy is that we do not impose parametric modeling assumptions on the outcome variables, making it more versatile and applicable to a wider array of applications. Through our theoretical investigation, we characterize the convergence rate of the estimated treatment effects and the associated standard deviations at the group level and further prove that our adaptive treatment assignment algorithm, despite not having a closed-form expression, approaches the optimal allocation rule asymptotically. Our proof strategy takes into account the fact that the allocation decisions in our design depend on sequentially accumulated data, which poses a significant challenge in characterizing the properties and conducting statistical inference of our method. We further provide simulation evidence and two synthetic data studies to showcase the performance of our fair adaptive experiment strategy.

As a classical generative modeling approach, energy-based models have the natural advantage of flexibility in the form of the energy function. Recently, energy-based models have achieved great success in modeling high-dimensional data in computer vision and natural language processing. In line with these advancements, we build a multi-purpose energy-based probabilistic model for High Energy Physics events at the Large Hadron Collider. This framework builds on a powerful generative model and describes higher-order inter-particle interactions. It suits different encoding architectures and builds on implicit generation. As for applicational aspects, it can serve as a powerful parameterized event generator for physics simulation, a generic anomalous signal detector free from spurious correlations, and an augmented event classifier for particle identification.

Sequential latent variable models (SLVMs) are essential tools in statistics and machine learning, with applications ranging from healthcare to neuroscience. As their flexibility increases, analytic inference and model learning can become challenging, necessitating approximate methods. Here we introduce neural adaptive smoothing via twisting (NAS-X), a method that extends reweighted wake-sleep (RWS) to the sequential setting by using smoothing sequential Monte Carlo (SMC) to estimate intractable posterior expectations. Combining RWS and smoothing SMC allows NAS-X to provide low-bias and low-variance gradient estimates, and fit both discrete and continuous latent variable models. We illustrate the theoretical advantages of NAS-X over previous methods and explore these advantages empirically in a variety of tasks, including a challenging application to mechanistic models of neuronal dynamics. These experiments show that NAS-X substantially outperforms previous VI- and RWS-based methods in inference and model learning, achieving lower parameter error and tighter likelihood bounds.

Generative models of observations under interventions have been a vibrant topic of interest across machine learning and the sciences in recent years. For example, in drug discovery, there is a need to model the effects of diverse interventions on cells in order to characterize unknown biological mechanisms of action. We propose the Sparse Additive Mechanism Shift Variational Autoencoder, SAMS-VAE, to combine compositionality, disentanglement, and interpretability for perturbation models. SAMS-VAE models the latent state of a perturbed sample as the sum of a local latent variable capturing sample-specific variation and sparse global variables of latent intervention effects. Crucially, SAMS-VAE sparsifies these global latent variables for individual perturbations to identify disentangled, perturbation-specific latent subspaces that are flexibly composable. We evaluate SAMS-VAE both quantitatively and qualitatively on a range of tasks using two popular single cell sequencing datasets. In order to measure perturbation-specific model-properties, we also introduce a framework for evaluation of perturbation models based on average treatment effects with links to posterior predictive checks. SAMS-VAE outperforms comparable models in terms of generalization across in-distribution and out-of-distribution tasks, including a combinatorial reasoning task under resource paucity, and yields interpretable latent structures which correlate strongly to known biological mechanisms. Our results suggest SAMS-VAE is an interesting addition to the modeling toolkit for machine learning-driven scientific discovery.

Symmetries have been leveraged to improve the generalization of neural networks through different mechanisms from data augmentation to equivariant architectures. However, despite their potential, their integration into neural solvers for partial differential equations (PDEs) remains largely unexplored. We explore the integration of PDE symmetries, known as Lie point symmetries, in a major family of neural solvers known as physics-informed neural networks (PINNs). We propose a loss function that informs the network about Lie point symmetries in the same way that PINN models try to enforce the underlying PDE through a loss function. Intuitively, our symmetry loss ensures that the infinitesimal generators of the Lie group conserve the PDE solutions.. Effectively, this means that once the network learns a solution, it also learns the neighbouring solutions generated by Lie point symmetries. Empirical evaluations indicate that the inductive bias introduced by the Lie point symmetries of the PDEs greatly boosts the sample efficiency of PINNs.

Inductive Conformal Prediction (ICP) provides a practical and effective approach for equipping deep learning models with uncertainty estimates in the form of set-valued predictions which are guaranteed to contain the ground truth with high probability. Despite the appeal of this coverage guarantee, these sets may not be efficient: the size and contents of the prediction sets are not directly controlled, and instead depend on the underlying model and choice of score function. To remedy this, recent work has proposed learning model and score function parameters using data to directly optimize the efficiency of the ICP prediction sets. While appealing, the generalization theory for such an approach is lacking: direct optimization of empirical efficiency may yield prediction sets that are either no longer efficient on test data, or no longer obtain the required coverage on test data. In this work, we use PAC-Bayes theory to obtain generalization bounds on both the coverage and the efficiency of set-valued predictors which can be directly optimized to maximize efficiency while satisfying a desired test coverage. In contrast to prior work, our framework allows us to utilize the entire calibration dataset to learn the parameters of the model and score function, instead of requiring a separate hold-out set for obtaining test-time coverage guarantees. We leverage these theoretical results to provide a practical algorithm for using calibration data to simultaneously fine-tune the parameters of a model and score function while guaranteeing test-time coverage and efficiency of the resulting prediction sets. We evaluate the approach on regression and classification tasks, and outperform baselines calibrated using a Hoeffding bound-based PAC guarantee on ICP, especially in the low-data regime.

Conformal inference provides a general distribution-free method to rigorously calibrate the output of any machine learning algorithm for novelty detection. While this approach has many strengths, it has the limitation of being randomized, in the sense that it may lead to different results when analyzing twice the same data and this can hinder the interpretation of any findings. We propose to make conformal inferences more stable by leveraging suitable conformal e-values instead of p-values to quantify statistical significance. This solution allows the evidence gathered from multiple analyses of the same data to be aggregated effectively while provably controlling the false discovery rate. Further, we show that the proposed method can reduce randomness without much loss of power compared to standard conformal inference, partly thanks to an innovative way of weighting conformal e-values based on additional side information carefully extracted from the same data. Simulations with synthetic and real data confirm this solution can be effective at eliminating random noise in the inferences obtained with state-of-the-art alternative techniques, sometimes also leading to higher power.

To check the accuracy of Bayesian computations, it is common to use rank-based simulation-based calibration (SBC). However, SBC has drawbacks: The test statistic is somewhat ad-hoc, interactions are difficult to examine, multiple testing is a challenge, and the resulting p-value is not a divergence metric. We propose to replace the marginal rank test with a flexible classification approach that learns test statistics from data. This measure typically has a higher statistical power than the SBC test and returns an interpretable divergence measure of miscalibration, computed from classification accuracy. This approach can be used with different data generating processes to address simulation-based inference or traditional inference methods like Markov chain Monte Carlo or variational inference. We illustrate an automated implementation using neural networks and statistically-inspired features, and validate the method with numerical and real data experiments.

Temporal difference (TD) learning is often used to update the estimate of the value function which is used by RL agents to extract useful policies. In this paper, we focus on value function estimation in continual reinforcement learning. We propose to decompose the value function into two components which update at different timescales: a _permanent_ value function, which holds general knowledge that persists over time, and a _transient_ value function, which allows quick adaptation to new situations. We establish theoretical results showing that our approach is well suited for continual learning and draw connections to the complementary learning systems (CLS) theory from neuroscience. Empirically, this approach improves performance significantly on both prediction and control problems.

We present a new representation learning framework, Intensity Profile Projection, for continuous-time dynamic network data. Given triples $(i,j,t)$, each representing a time-stamped ($t$) interaction between two entities ($i,j$), our procedure returns a continuous-time trajectory for each node, representing its behaviour over time. The framework consists of three stages: estimating pairwise intensity functions, e.g. via kernel smoothing; learning a projection which minimises a notion of intensity reconstruction error; and constructing evolving node representations via the learned projection. The trajectories satisfy two properties, known as structural and temporal coherence, which we see as fundamental for reliable inference. Moreoever, we develop estimation theory providing tight control on the error of any estimated trajectory, indicating that the representations could even be used in quite noise-sensitive follow-on analyses. The theory also elucidates the role of smoothing as a bias-variance trade-off, and shows how we can reduce the level of smoothing as the signal-to-noise ratio increases on account of the algorithm `borrowing strength' across the network.

The gold standard for causal model evaluation involves comparing model predictions with true effects estimated from randomized controlled trials (RCT). However, RCTs are not always feasible or ethical to perform. In contrast, conditionally randomized experiments based on inverse probability weighting (IPW) offer a more realistic approach but may suffer from high estimation variance. To tackle this challenge and enhance causal model evaluation in real-world conditional randomization settings, we introduce a novel low-variance estimator for causal error, dubbed as the pairs estimator. By applying the same IPW estimator to both the model and true experimental effects, our estimator effectively cancels out the variance due to IPW and achieves a smaller asymptotic variance. Empirical studies demonstrate the improved of our estimator, highlighting its potential on achieving near-RCT performance. Our method offers a simple yet powerful solution to evaluate causal inference models in conditional randomization settings without complicated modification of the IPW estimator itself, paving the way for more robust and reliable model assessments.

A potent class of generative models known as Diffusion Probabilistic Models (DPMs) has become prominent. A forward diffusion process adds gradually noise to data, while a model learns to gradually denoise. Sampling from pre-trained DPMs is obtained by solving differential equations (DE) defined by the learnt model, a process which has shown to be prohibitively slow. Numerous efforts on speeding-up this process have consisted on crafting powerful ODE solvers. Despite being quick, such solvers do not usually reach the optimal quality achieved by available slow SDE solvers. Our goal is to propose SDE solvers that reach optimal quality without requiring several hundreds or thousands of NFEs to achieve that goal. We propose Stochastic Explicit Exponential Derivative-free Solvers (SEEDS), improving and generalizing Exponential Integrator approaches to the stochastic case on several frameworks. After carefully analyzing the formulation of exact solutions of diffusion SDEs, we craft SEEDS to analytically compute the linear part of such solutions. Inspired by the Exponential Time-Differencing method, SEEDS use a novel treatment of the stochastic components of solutions, enabling the analytical computation of their variance, and contains high-order terms allowing to reach optimal quality sampling $\sim3$-$5\times$ faster than previous SDE methods. We validate our approach on several image generation benchmarks, showing that SEEDS outperform or are competitive with previous SDE solvers. Contrary to the latter, SEEDS are derivative and training free, and we fully prove strong convergence guarantees for them.

We propose a notion of common information that allows one to quantify and separate the information that is shared between two random variables from the information that is unique to each. Our notion of common information is defined by an optimization problem over a family of functions and recovers the G\'acs-K\"orner common information as a special case. Importantly, our notion can be approximated empirically using samples from the underlying data distribution. We then provide a method to partition and quantify the common and unique information using a simple modification of a traditional variational auto-encoder. Empirically, we demonstrate that our formulation allows us to learn semantically meaningful common and unique factors of variation even on high-dimensional data such as images and videos. Moreover, on datasets where ground-truth latent factors are known, we show that we can accurately quantify the common information between the random variables.

Learning cause and effect relations is arguably one of the central challenges found throughout the data sciences. Formally, determining whether a collection of observational and interventional distributions can be combined to learn a target causal relation is known as the problem of generalized identification (or g-identification) [Lee et al., 2019]. Although g-identification has been well understood and solved in theory, it turns out to be challenging to apply these results in practice, in particular when considering the estimation of the target distribution from finite samples. In this paper, we develop a new, general estimator that exhibits multiply robustness properties for g-identifiable causal functionals. Specifically, we show that any g-identifiable causal effect can be expressed as a function of generalized multi-outcome sequential back-door adjustments that are amenable to estimation. We then construct a corresponding estimator for the g-identification expression that exhibits robustness properties to bias. We analyze the asymptotic convergence properties of the estimator. Finally, we illustrate the use of the proposed estimator in experimental studies. Simulation results corroborate the theory.

Survival analysis is a crucial semi-supervised task in machine learning with significant real-world applications, especially in healthcare. The most common approach to survival analysis, Cox’s partial likelihood, can be interpreted as a ranking model optimized on a lower bound of the concordance index. We follow these connections further, with listwise ranking losses that allow for a relaxation of the pairwise independence assumption. Given the inherent transitivity of ranking, we explore differentiable sorting networks as a means to introduce a stronger transitive inductive bias during optimization. Despite their potential, current differentiable sorting methods cannot account for censoring, a crucial aspect of many real-world datasets. We propose a novel method, Diffsurv, to overcome this limitation by extending differentiable sorting methods to handle censored tasks. Diffsurv predicts matrices of possible permutations that accommodate the label uncertainty introduced by censored samples. Our experiments reveal that Diffsurv outperforms established baselines in various simulated and real-world risk prediction scenarios. Furthermore, we demonstrate the algorithmic advantages of Diffsurv by presenting a novel method for top-k risk prediction that surpasses current methods.

Discovering causal relations from observational time series without making the stationary assumption is a significant challenge. In practice, this challenge is common in many areas, such as retail sales, transportation systems, and medical science. Here, we consider this problem for a class of non-stationary time series problems. The structural causal model (SCM) of this type of time series, called the semi-stationary time series, exhibits that a finite number of different causal mechanisms occur sequentially and periodically across time. This model holds considerable practical utility because it can represent periodicity, including common occurrences such as seasonality and diurnal variation. We propose a constraint-based, non-parametric algorithm for discovering causal relations in this setting. The resulting algorithm, PCMCI$_{\Omega}$, can capture the alternating and recurring changes in the causal mechanisms and then identify the underlying causal graph with conditional independence (CI) tests. We show that this algorithm is sound in identifying causal relations on discrete time series. We validate the algorithm with extensive experiments on continuous and discrete simulated data. We also apply our algorithm to a real-world climate dataset.

We introduce Resilient Multiple Choice Learning (rMCL), an extension of the MCL approach for conditional distribution estimation in regression settings where multiple targets may be sampled for each training input. Multiple Choice Learning is a simple framework to tackle multimodal density estimation, using the Winner-Takes-All (WTA) loss for a set of hypotheses. In regression settings, the existing MCL variants focus on merging the hypotheses, thereby eventually sacrificing the diversity of the predictions. In contrast, our method relies on a novel learned scoring scheme underpinned by a mathematical framework based on Voronoi tessellations of the output space, from which we can derive a probabilistic interpretation. After empirically validating rMCL with experiments on synthetic data, we further assess its merits on the sound source localization problem, demonstrating its practical usefulness and the relevance of its interpretation.

Learning graphical conditional independence structures is an important machine learning problem and a cornerstone of causal discovery. However, the accuracy and execution time of learning algorithms generally struggle to scale to problems with hundreds of highly connected variables---for instance, recovering brain networks from fMRI data. We introduce the best order score search (BOSS) and grow-shrink trees (GSTs) for learning directed acyclic graphs (DAGs) in this paradigm. BOSS greedily searches over permutations of variables, using GSTs to construct and score DAGs from permutations. GSTs efficiently cache scores to eliminate redundant calculations. BOSS achieves state-of-the-art performance in accuracy and execution time, comparing favorably to a variety of combinatorial and gradient-based learning algorithms under a broad range of conditions. To demonstrate its practicality, we apply BOSS to two sets of resting-state fMRI data: simulated data with pseudo-empirical noise distributions derived from randomized empirical fMRI cortical signals and clinical data from 3T fMRI scans processed into cortical parcels. BOSS is available for use within the TETRAD project which includes Python and R wrappers.

We developed a new method PROTES for black-box optimization, which is based on the probabilistic sampling from a probability density function given in the low-parametric tensor train format. We tested it on complex multidimensional arrays and discretized multivariable functions taken, among others, from real-world applications, including unconstrained binary optimization and optimal control problems, for which the possible number of elements is up to $2^{1000}$. In numerical experiments, both on analytic model functions and on complex problems, PROTES outperforms popular discrete optimization methods (Particle Swarm Optimization, Covariance Matrix Adaptation, Differential Evolution, and others).

By now Bayesian methods are routinely used in practice for solving inverse problems. In inverse problems the parameter or signal of interest is observed only indirectly, as an image of a given map, and the observations are typically further corrupted with noise. Bayes offers a natural way to regularize these problems via the prior distribution and provides a probabilistic solution, quantifying the remaining uncertainty in the problem. However, the computational costs of standard, sampling based Bayesian approaches can be overly large in such complex models. Therefore, in practice variational Bayes is becoming increasingly popular. Nevertheless, the theoretical understanding of these methods is still relatively limited, especially in context of inverse problems. In our analysis we investigate variational Bayesian methods for Gaussian process priors to solve linear inverse problems. We consider both mildly and severely ill-posed inverse problems and work with the popular inducing variable variational Bayes approach proposed by Titsias [Titsias, 2009]. We derive posterior contraction rates for the variational posterior in general settings and show that the minimax estimation rate can be attained by correctly tunned procedures. As specific examples we consider a collection of inverse problems including the heat equation, Volterra operator and Radon transform and inducing variable methods based on population and empirical spectral features.

Feedforward generalizable models for implicit shape reconstruction from unoriented point cloud present multiple advantages, including high performance and inference speed. However, they still suffer from generalization issues, ranging from underfitting the input point cloud, to misrepresenting samples outside of the training data distribution, or with toplogies unseen at training. We propose here an efficient mechanism to remedy some of these limitations at test time. We combine the inter-shape data prior of the network with an intra-shape regularization prior of a Nyström Kernel Ridge Regression, that we further adapt by fitting its hyperprameters to the current shape. The resulting shape function defined in a shape specific Reproducing Kernel Hilbert Space benefits from desirable stability and efficiency properties and grants a shape adaptive expressiveness-robustness trade-off. We demonstrate the improvement obtained through our method with respect to baselines and the state-of-the-art using synthetic and real data.

Segmentation of curvilinear structures such as vasculature and road networks is challenging due to relatively weak signals and complex geometry/topology. To facilitate and accelerate large scale annotation, one has to adopt semi-automatic approaches such as proofreading by experts. In this work, we focus on uncertainty estimation for such tasks, so that highly uncertain, and thus error-prone structures can be identified for human annotators to verify. Unlike most existing works, which provide pixel-wise uncertainty maps, we stipulate it is crucial to estimate uncertainty in the units of topological structures, e.g., small pieces of connections and branches. To achieve this, we leverage tools from topological data analysis, specifically discrete Morse theory (DMT), to first capture the structures, and then reason about their uncertainties. To model the uncertainty, we (1) propose a joint prediction model that estimates the uncertainty of a structure while taking the neighboring structures into consideration (inter-structural uncertainty); (2) propose a novel Probabilistic DMT to model the inherent uncertainty within each structure (intra-structural uncertainty) by sampling its representations via a perturb-and-walk scheme. On various 2D and 3D datasets, our method produces better structure-wise uncertainty maps compared to existing works. Code available at: https://github.com/Saumya-Gupta-26/struct-uncertainty

Point clouds are versatile representations of 3D objects and have found widespread application in science and engineering. Many successful deep-learning models have been proposed that use them as input. The domain of chemical and materials modeling is especially challenging because exact compliance with physical constraints is highly desirable for a model to be usable in practice. These constraints include smoothness and invariance with respect to translations, rotations, and permutations of identical atoms. If these requirements are not rigorously fulfilled, atomistic simulations might lead to absurd outcomes even if the model has excellent accuracy. Consequently, dedicated architectures, which achieve invariance by restricting their design space, have been developed. General-purpose point-cloud models are more varied but often disregard rotational symmetry. We propose a general symmetrization method that adds rotational equivariance to any given model while preserving all the other requirements. Our approach simplifies the development of better atomic-scale ML schemes by relaxing the constraints on the design space and making it possible to incorporate ideas that proved effective in other domains. We demonstrate this idea by introducing the Point Edge Transformer (PET) architecture, which is not intrinsically equivariant but achieves state-of-the-art performance on several benchmark datasets of molecules and solids. A-posteriori application of our general protocol makes PET exactly equivariant, with minimal changes to its accuracy.

Motivated by a recent literature on the double-descent phenomenon in machine learning, we consider highly over-parameterized models in causal inference, including synthetic control with many control units. In such models, there may be so many free parameters that the model fits the training data perfectly. We first investigate high-dimensional linear regression for imputing wage data and estimating average treatment effects, where we find that models with many more covariates than sample size can outperform simple ones. We then document the performance of high-dimensional synthetic control estimators with many control units. We find that adding control units can help improve imputation performance even beyond the point where the pre-treatment fit is perfect. We provide a unified theoretical perspective on the performance of these high-dimensional models. Specifically, we show that more complex models can be interpreted as model-averaging estimators over simpler ones, which we link to an improvement in average performance. This perspective yields concrete insights into the use of synthetic control when control units are many relative to the number of pre-treatment periods.

We consider the problem of variational Bayesian inference in a latent variable model where a (possibly complex) observed stochastic process is governed by the unobserved solution of a latent stochastic differential equation (SDE). Motivated by the challenges that arise when trying to learn a latent SDE in $\mathbb{R}^n$ from large-scale data, such as efficient gradient computation, we take a step back and study a specific subclass instead. In our case, the SDE evolves inside a homogeneous latent space and is induced by stochastic dynamics of the corresponding (matrix) Lie group. In the context of learning problems, SDEs on the $n$-dimensional unit sphere are arguably the most relevant incarnation of this setup. For variational inference, the sphere not only facilitates using a uniform prior on the initial state of the SDE, but we also obtain a particularly simple and intuitive expression for the KL divergence between the approximate posterior and prior process in the evidence lower bound. We provide empirical evidence that a latent SDE of the proposed type can be learned efficiently by means of an existing one-step geometric Euler-Maruyama scheme. Despite restricting ourselves to a less diverse class of SDEs, we achieve competitive or even state-of-the-art performance on a collection of time series interpolation and classification benchmarks.

Bayesian brain theory suggests that the brain employs generative models to understand the external world. The sampling-based perspective posits that the brain infers the posterior distribution through samples of stochastic neuronal responses. Additionally, the brain continually updates its generative model to approach the true distribution of the external world. In this study, we introduce the Hierarchical Exponential-family Energy-based (HEE) model, which captures the dynamics of inference and learning. In the HEE model, we decompose the partition function into individual layers and leverage a group of neurons with shorter time constants to sample the gradient of the decomposed normalization term. This allows our model to estimate the partition function and perform inference simultaneously, circumventing the negative phase encountered in conventional energy-based models (EBMs). As a result, the learning process is localized both in time and space, and the model is easy to converge. To match the brain's rapid computation, we demonstrate that neural adaptation can serve as a momentum term, significantly accelerating the inference process. On natural image datasets, our model exhibits representations akin to those observed in the biological visual system. Furthermore, for the machine learning community, our model can generate observations through joint or marginal generation. We show that marginal generation outperforms joint generation and achieves performance on par with other EBMs.

An important problem in time-series analysis is modeling systems with time-varying dynamics. Probabilistic models with joint continuous and discrete latent states offer interpretable, efficient, and experimentally useful descriptions of such data. Commonly used models include autoregressive hidden Markov models (ARHMMs) and switching linear dynamical systems (SLDSs), each with its own advantages and disadvantages. ARHMMs permit exact inference and easy parameter estimation, but are parameter intensive when modeling long dependencies, and hence are prone to overfitting. In contrast, SLDSs can capture long-range dependencies in a parameter efficient way through Markovian latent dynamics, but present an intractable likelihood and a challenging parameter estimation task. In this paper, we propose _switching autoregressive low-rank tensor_ SALT models, which retain the advantages of both approaches while ameliorating the weaknesses. SALT parameterizes the tensor of an ARHMM with a low-rank factorization to control the number of parameters and allow longer range dependencies without overfitting. We prove theoretical and discuss practical connections between SALT, linear dynamical systems, and SLDSs. We empirically demonstrate quantitative advantages of SALT models on a range of simulated and real prediction tasks, including behavioral and neural datasets. Furthermore, the learned low-rank tensor provides novel insights into temporal dependencies within each discrete state.

People are adept at learning a wide variety of structured patterns from small amounts of data, presenting a conundrum from the standpoint of the bias-variance tradeoff: what kinds of representations and algorithms support the joint flexibility and data-paucity of human learning? One possibility is that people "learn by programming": inducing probabilistic models to fit observed data. Here, we experimentally test human learning in the domain of structured 2-dimensional patterns, using a task in which participants repeatedly predicted where a dot would move based on its previous trajectory. We evaluate human performance against standard parametric and non-parametric time-series models, as well as two Bayesian program synthesis models whose hypotheses vary in their degree of structure: a compositional Gaussian Process model and a structured "Language of Thought" (LoT) model. We find that signatures of human pattern learning are best explained by the LoT model, supporting the idea that the flexibility and data-efficiency of human structure learning can be understood as probabilistic inference over an expressive space of programs.

Quantifying uncertainty is important for actionable predictions in real-world applications. A crucial part of predictive uncertainty quantification is the estimation of epistemic uncertainty, which is defined as an integral of the product between a divergence function and the posterior. Current methods such as Deep Ensembles or MC dropout underperform at estimating the epistemic uncertainty, since they primarily consider the posterior when sampling models. We suggest Quantification of Uncertainty with Adversarial Models (QUAM) to better estimate the epistemic uncertainty. QUAM identifies regions where the whole product under the integral is large, not just the posterior. Consequently, QUAM has lower approximation error of the epistemic uncertainty compared to previous methods. Models for which the product is large correspond to adversarial models (not adversarial examples!). Adversarial models have both a high posterior as well as a high divergence between their predictions and that of a reference model. Our experiments show that QUAM excels in capturing epistemic uncertainty for deep learning models and outperforms previous methods on challenging tasks in the vision domain.

Recent research indicates that the performance of machine learning models can be improved by aligning the geometry of the latent space with the underlying data structure. Rather than relying solely on Euclidean space, researchers have proposed using hyperbolic and spherical spaces with constant curvature, or combinations thereof, to better model the latent space and enhance model performance. However, little attention has been given to the problem of automatically identifying the optimal latent geometry for the downstream task. We mathematically define this novel formulation and coin it as neural latent geometry search (NLGS). More specifically, we introduce an initial attempt to search for a latent geometry composed of a product of constant curvature model spaces with a small number of query evaluations, under some simplifying assumptions. To accomplish this, we propose a novel notion of distance between candidate latent geometries based on the Gromov-Hausdorff distance from metric geometry. In order to compute the Gromov-Hausdorff distance, we introduce a mapping function that enables the comparison of different manifolds by embedding them in a common high-dimensional ambient space. We then design a graph search space based on the notion of smoothness between latent geometries and employ the calculated distances as an additional inductive bias. Finally, we use Bayesian optimization to search for the optimal latent geometry in a query-efficient manner. This is a general method which can be applied to search for the optimal latent geometry for a variety of models and downstream tasks. We perform experiments on synthetic and real-world datasets to identify the optimal latent geometry for multiple machine learning problems.

Predominately in explainable artificial intelligence (XAI) research, the Shapley value (SV) is applied to determine feature attributions for any black box model. Shapley interaction indices extend the SV to define any-order feature interactions. Defining a unique Shapley interaction index is an open research question and, so far, three definitions have been proposed, which differ by their choice of axioms. Moreover, each definition requires a specific approximation technique. Here, we propose SHAPley Interaction Quantification (SHAP-IQ), an efficient sampling-based approximator to compute Shapley interactions for arbitrary cardinal interaction indices (CII), i.e. interaction indices that satisfy the linearity, symmetry and dummy axiom. SHAP-IQ is based on a novel representation and, in contrast to existing methods, we provide theoretical guarantees for its approximation quality, as well as estimates for the variance of the point estimates. For the special case of SV, our approach reveals a novel representation of the SV and corresponds to Unbiased KernelSHAP with a greatly simplified calculation. We illustrate the computational efficiency and effectiveness by explaining language, image classification and high-dimensional synthetic models.

Variable importance assessment has become a crucial step in machine-learning applications when using complex learners, such as deep neural networks, on large-scale data. Removal-based importance assessment is currently the reference approach, particularly when statistical guarantees are sought to justify variable inclusion. It is often implemented with variable permutation schemes. On the flip side, these approaches risk misidentifying unimportant variables as important in the presence of correlations among covariates. Here we develop a systematic approach for studying Conditional Permutation Importance (CPI) that is model agnostic and computationally lean, as well as reusable benchmarks of state-of-the-art variable importance estimators. We show theoretically and empirically that \textit{CPI} overcomes the limitations of standard permutation importance by providing accurate type-I error control. When used with a deep neural network, \textit{CPI} consistently showed top accuracy across benchmarks. An experiment on real-world data analysis in a large-scale medical dataset showed that \textit{CPI} provides a more parsimonious selection of statistically significant variables. Our results suggest that \textit{CPI} can be readily used as drop-in replacement for permutation-based methods.

Incorporating geometric inductive biases into models can aid interpretability and generalization, but encoding to a specific geometric structure can be challenging due to the imposed topological constraints. In this paper, we theoretically and empirically characterize obstructions to training encoders with geometric latent spaces. We show that local optima can arise due to singularities (e.g. self-intersection) or due to an incorrect degree or winding number. We then discuss how normalizing flows can potentially circumvent these obstructions by defining multimodal variational distributions. Inspired by this observation, we propose a new flow-based model that maps data points to multimodal distributions over geometric spaces and empirically evaluate our model on 2 domains. We observe improved stability during training and a higher chance of converging to a homeomorphic encoder.

We introduce a new type of query mechanism for collecting human feedback, called the perceptual adjustment query (PAQ). Being both informative and cognitively lightweight, the PAQ adopts an inverted measurement scheme, and combines advantages from both cardinal and ordinal queries. We showcase the PAQ in the metric learning problem, where we collect PAQ measurements to learn an unknown Mahalanobis distance. This gives rise to a high-dimensional, low-rank matrix estimation problem to which standard matrix estimators cannot be applied. Consequently, we develop a two-stage estimator for metric learning from PAQs, and provide sample complexity guarantees for this estimator. We present numerical simulations demonstrating the performance of the estimator and its notable properties.

Many problems in Reinforcement Learning (RL) seek an optimal policy with large discrete multidimensional yet unordered action spaces; these include problems in randomized allocation of resources such as placements of multiple security resources and emergency response units, etc. A challenge in this setting is that the underlying action space is categorical (discrete and unordered) and large, for which existing RL methods do not perform well. Moreover, these problems require validity of the realized action (allocation); this validity constraint is often difficult to express compactly in a closed mathematical form. The allocation nature of the problem also prefers stochastic optimal policies, if one exists. In this work, we address these challenges by (1) applying a (state) conditional normalizing flow to compactly represent the stochastic policy — the compactness arises due to the network only producing one sampled action and the corresponding log probability of the action, which is then used by an actor-critic method; and (2) employing an invalid action rejection method (via a valid action oracle) to update the base policy. The action rejection is enabled by a modified policy gradient that we derive. Finally, we conduct extensive experiments to show the scalability of our approach compared to prior methods and the ability to enforce arbitrary state-conditional constraints on the support of the distribution of actions in any state.

Closed-form differential equations, including partial differential equations and higher-order ordinary differential equations, are one of the most important tools used by scientists to model and better understand natural phenomena. Discovering these equations directly from data is challenging because it requires modeling relationships between various derivatives that are not observed in the data (equation-data mismatch) and it involves searching across a huge space of possible equations. Current approaches make strong assumptions about the form of the equation and thus fail to discover many well-known phenomena. Moreover, many of them resolve the equation-data mismatch by estimating the derivatives, which makes them inadequate for noisy and infrequent observations. To this end, we propose D-CIPHER, which is robust to measurement artifacts and can uncover a new and very general class of differential equations. We further design a novel optimization procedure, CoLLie, to help D-CIPHER search through this class efficiently. Finally, we demonstrate empirically that it can discover many well-known equations that are beyond the capabilities of current methods.

Deep Neural Networks (DNNs) demonstrated remarkable capabilities in learning complex hierarchical data representations, but the nature of these representations remains largely unknown. Existing global explainability methods, such as Network Dissection, face limitations such as reliance on segmentation masks, lack of statistical significance testing, and high computational demands. We propose Inverse Recognition (INVERT), a scalable approach for linking the learned representations to human-interpretable concepts based on the ability to differentiate between concepts. In contrast to prior work, INVERT is capable of handling diverse types of neurons, exhibits less computational complexity, and does not rely on the availability of segmentation masks. Moreover, INVERT provides an interpretable metric assessing the alignment between the representation and its corresponding explanation and delivering a measure of statistical significance, emphasizing its utility and credibility. We demonstrate the applicability of INVERT in various scenarios, including the identification of representations affected by spurious correlations, and the interpretation of the hierarchical structure of decision-making within the models.

The Kohn-Sham equations underlie many important applications such as the discovery of new catalysts. Recent machine learning work on catalyst modeling has focused on prediction of the energy, but has so far not yet demonstrated significant out-of-distribution generalization. Here we investigate another approach based on the pointwise learning of the Kohn-Sham charge-density. On a new dataset of bulk catalysts with charge densities, we show density models can generalize to new structures with combinations of elements not seen at train time, a form of combinatorial generalization. We show that over 80% of binary and ternary test cases achieve faster convergence than standard baselines in Density Functional Theory, amounting to an average reduction of 13% in the number of iterations required to reach convergence, which may be of independent interest. Our results suggest that density learning is a viable alternative, trading greater inference costs for a step towards combinatorial generalization, a key property for applications.

In this paper, we propose a novel and powerful method to harness Bayesian optimization for variational quantum eigensolvers (VQEs) - a hybrid quantum-classical protocol used to approximate the ground state of a quantum Hamiltonian. Specifically, we derive a *VQE-kernel* which incorporates important prior information about quantum circuits: the kernel feature map of the VQE-kernel exactly matches the known functional form of the VQE's objective function and thereby significantly reduces the posterior uncertainty. Moreover, we propose a novel acquisition function for Bayesian optimization called \emph{Expected Maximum Improvement over Confident Regions} (EMICoRe) which can actively exploit the inductive bias of the VQE-kernel by treating regions with low predictive uncertainty as indirectly "observed". As a result, observations at as few as three points in the search domain are sufficient to determine the complete objective function along an entire one-dimensional subspace of the optimization landscape. Our numerical experiments demonstrate that our approach improves over state-of-the-art baselines.

Causal identification is at the core of the causal inference literature, where complete algorithms have been proposed to identify causal queries of interest. The validity of these algorithms hinges on the restrictive assumption of having access to a correctly specified causal structure. In this work, we study the setting where a probabilistic model of the causal structure is available. Specifically, the edges in a causal graph exist with uncertainties which may, for example, represent degree of belief from domain experts. Alternatively, the uncertainty about an edge may reflect the confidence of a particular statistical test. The question that naturally arises in this setting is: Given such a probabilistic graph and a specific causal effect of interest, what is the subgraph which has the highest plausibility and for which the causal effect is identifiable? We show that answering this question reduces to solving an NP-hard combinatorial optimization problem which we call the edge ID problem. We propose efficient algorithms to approximate this problem and evaluate them against both real-world networks and randomly generated graphs.

Energy-based models (EBMs) are generative models inspired by statistical physics with a wide range of applications in unsupervised learning. Their performance is well measured by the cross-entropy (CE) of the model distribution relative to the data distribution. Using the CE as the objective for training is however challenging because the computation of its gradient with respect to the model parameters requires sampling the model distribution. Here we show how results for nonequilibrium thermodynamics based on Jarzynski equality together with tools from sequential Monte-Carlo sampling can be used to perform this computation efficiently and avoid the uncontrolled approximations made using the standard contrastive divergence algorithm. Specifically, we introduce a modification of the unadjusted Langevin algorithm (ULA) in which each walker acquires a weight that enables the estimation of the gradient of the cross-entropy at any step during GD, thereby bypassing sampling biases induced by slow mixing of ULA. We illustrate these results with numerical experiments on Gaussian mixture distributions as well as the MNIST and CIFAR-10 datasets. We show that the proposed approach outperforms methods based on the contrastive divergence algorithm in all the considered situations.

Models that rely solely on pairwise relationships often fail to capture the complete statistical structure of the complex multivariate data found in diverse domains, such as socio-economic, ecological, or biomedical systems. Non-trivial dependencies between groups of more than two variables can play a significant role in the analysis and modelling of such systems, yet extracting such high-order interactions from data remains challenging. Here, we introduce a hierarchy of $d$-order ($d \geq 2$) interaction measures, increasingly inclusive of possible factorisations of the joint probability distribution, and define non-parametric, kernel-based tests to establish systematically the statistical significance of $d$-order interactions. We also establish mathematical links with lattice theory, which elucidate the derivation of the interaction measures and their composite permutation tests; clarify the connection of simplicial complexes with kernel matrix centring; and provide a means to enhance computational efficiency. We illustrate our results numerically with validations on synthetic data, and through an application to neuroimaging data.

The efficient coding hypothesis proposes that the response properties of sensory systems are adapted to the statistics of their inputs such that they capture maximal information about the environment, subject to biological constraints. While elegant, information theoretic properties are notoriously difficult to measure in practical settings or to employ as objective functions in optimization. This difficulty has necessitated that computational models designed to test the hypothesis employ several different information metrics ranging from approximations and lower bounds to proxy measures like reconstruction error. Recent theoretical advances have characterized a novel and ecologically relevant efficiency metric, the ``manifold capacity,” which is the number of object categories that may be represented in a linearly separable fashion. However, calculating manifold capacity is a computationally intensive iterative procedure that until now has precluded its use as an objective. Here we outline the simplifying assumptions that allow manifold capacity to be optimized directly, yielding Maximum Manifold Capacity Representations (MMCR). The resulting method is closely related to and inspired by advances in the field of self supervised learning (SSL), and we demonstrate that MMCRs are competitive with state of the art results on standard SSL benchmarks. Empirical analyses reveal differences between MMCRs and representations learned by other SSL frameworks, and suggest a mechanism by which manifold compression gives rise to class separability. Finally we evaluate a set of SSL methods on a suite of neural predicitivity benchmarks, and find MMCRs are higly competitive as models of the ventral stream.

Learning curve extrapolation aims to predict model performance in later epochs of training, based on the performance in earlier epochs. In this work, we argue that, while the inherent uncertainty in the extrapolation of learning curves warrants a Bayesian approach, existing methods are (i) overly restrictive, and/or (ii) computationally expensive. We describe the first application of prior-data fitted neural networks (PFNs) in this context. A PFN is a transformer, pre-trained on data generated from a prior, to perform approximate Bayesian inference in a single forward pass. We propose LC-PFN, a PFN trained to extrapolate 10 million artificial right-censored learning curves generated from a parametric prior proposed in prior art using MCMC. We demonstrate that LC-PFN can approximate the posterior predictive distribution more accurately than MCMC, while being over 10 000 times faster. We also show that the same LC-PFN achieves competitive performance extrapolating a total of 20 000 real learning curves from four learning curve benchmarks (LCBench, NAS-Bench-201, Taskset, and PD1) that stem from training a wide range of model architectures (MLPs, CNNs, RNNs, and Transformers) on 53 different datasets with varying input modalities (tabular, image, text, and protein data). Finally, we investigate its potential in the context of model selection and find that a simple LC-PFN based predictive early stopping criterion obtains 2 - 6x speed-ups on 45 of these datasets, at virtually no overhead.

We present new insights and a novel paradigm for learning implicit neural representations (INR) of shapes. In particular, we shed light on the popular eikonal loss used for imposing a signed distance function constraint in INR. We show analytically that as the representation power of the network increases, the optimization approaches a partial differential equation (PDE) in the continuum limit that is unstable. We show that this instability can manifest in existing network optimization, leading to irregularities in the reconstructed surface and/or convergence to sub-optimal local minima, and thus fails to capture fine geometric and topological structure. We show analytically how other terms added to the loss, currently used in the literature for other purposes, can actually eliminate these instabilities. However, such terms can over-regularize the surface, preventing the representation of fine shape detail. Based on a similar PDE theory for the continuum limit, we introduce a new regularization term that still counteracts the eikonal instability but without over-regularizing. Furthermore, since stability is now guaranteed in the continuum limit, this stabilization also allows for considering new network structures that are able to represent finer shape detail. We introduce such a structure based on quadratic layers. Experiments on multiple benchmark data sets show that our new regularization and network are able to capture more precise shape details and more accurate topology than existing state-of-the-art.

Injecting structure into neural networks enables learning functions that satisfy invariances with respect to subsets of inputs. For instance, when learning generative models using neural networks, it is advantageous to encode the conditional independence structure of observed variables, often in the form of Bayesian networks. We propose the Structured Neural Network (StrNN), which injects structure through masking pathways in a neural network. The masks are designed via a novel relationship we explore between neural network architectures and binary matrix factorization, to ensure that the desired independencies are respected. We devise and study practical algorithms for this otherwise NP-hard design problem based on novel objectives that control the model architecture. We demonstrate the utility of StrNN in three applications: (1) binary and Gaussian density estimation with StrNN, (2) real-valued density estimation with Structured Autoregressive Flows (StrAFs) and Structured Continuous Normalizing Flows (StrCNF), and (3) interventional and counterfactual analysis with StrAFs for causal inference. Our work opens up new avenues for learning neural networks that enable data-efficient generative modeling and the use of normalizing flows for causal effect estimation.

Transformer has shown state-of-the-art performance on various applications and has recently emerged as a promising tool for surrogate modeling of partial differential equations (PDEs). Despite the introduction of linear-complexity attention, applying Transformer to problems with a large number of grid points can be numerically unstable and computationally expensive. In this work, we propose Factorized Transformer (FactFormer), which is based on an axial factorized kernel integral. Concretely, we introduce a learnable projection operator that decomposes the input function into multiple sub-functions with one-dimensional domain. These sub-functions are then evaluated and used to compute the instance-based kernel with an axial factorized scheme. We showcase that the proposed model is able to simulate 2D Kolmogorov flow on a $256\times 256$ grid and 3D smoke buoyancy on a $64\times64\times64$ grid with good accuracy and efficiency. The proposed factorized scheme can serve as a computationally efficient low-rank surrogate for the full attention scheme when dealing with multi-dimensional problems.

Off-Policy Evaluation (OPE) in contextual bandits is crucial for assessing new policies using existing data without costly experimentation. However, current OPE methods, such as Inverse Probability Weighting (IPW) and Doubly Robust (DR) estimators, suffer from high variance, particularly in cases of low overlap between target and behaviour policies or large action and context spaces. In this paper, we introduce a new OPE estimator for contextual bandits, the Marginal Ratio (MR) estimator, which focuses on the shift in the marginal distribution of outcomes $Y$ instead of the policies themselves. Through rigorous theoretical analysis, we demonstrate the benefits of the MR estimator compared to conventional methods like IPW and DR in terms of variance reduction. Additionally, we establish a connection between the MR estimator and the state-of-the-art Marginalized Inverse Propensity Score (MIPS) estimator, proving that MR achieves lower variance among a generalized family of MIPS estimators. We further illustrate the utility of the MR estimator in causal inference settings, where it exhibits enhanced performance in estimating Average Treatment Effects (ATE). Our experiments on synthetic and real-world datasets corroborate our theoretical findings and highlight the practical advantages of the MR estimator in OPE for contextual bandits.

We propose a novel framework for analyzing the dynamics of distribution shift in real-world systems that captures the feedback loop between learning algorithms and the distributions on which they are deployed. Prior work largely models feedback-induced distribution shift as adversarial or via an overly simplistic distribution-shift structure. In contrast, we propose a coupled partial differential equation model that captures fine-grained changes in the distribution over time by accounting for complex dynamics that arise due to strategic responses to algorithmic decision-making, non-local endogenous population interactions, and other exogenous sources of distribution shift. We consider two common settings in machine learning: cooperative settings with information asymmetries, and competitive settings where a learner faces strategic users. For both of these settings, when the algorithm retrains via gradient descent, we prove asymptotic convergence of the retraining procedure to a steady-state, both in finite and in infinite dimensions, obtaining explicit rates in terms of the model parameters. To do so we derive new results on the convergence of coupled PDEs that extends what is known on multi-species systems. Empirically, we show that our approach captures well-documented forms of distribution shifts like polarization and disparate impacts that simpler models cannot capture.

The theory of Koopman operators allows to deploy non-parametric machine learning algorithms to predict and analyze complex dynamical systems. Estimators such as principal component regression (PCR) or reduced rank regression (RRR) in kernel spaces can be shown to provably learn Koopman operators from finite empirical observations of the system's time evolution. Scaling these approaches to very long trajectories is a challenge and requires introducing suitable approximations to make computations feasible. In this paper, we boost the efficiency of different kernel-based Koopman operator estimators using random projections (sketching). We derive, implement and test the new ``sketched'' estimators with extensive experiments on synthetic and large-scale molecular dynamics datasets. Further, we establish non asymptotic error bounds giving a sharp characterization of the trade-offs between statistical learning rates and computational efficiency. Our empirical and theoretical analysis shows that the proposed estimators provide a sound and efficient way to learn large scale dynamical systems. In particular our experiments indicate that the proposed estimators retain the same accuracy of PCR or RRR, while being much faster.

Engineering design problems frequently require solving systems of partial differential equations with boundary conditions specified on object geometries in the form of a triangular mesh. These boundary geometries are provided by a designer and are problem dependent. The efficiency of the design process greatly benefits from fast turnaround times when repeatedly solving PDEs on various geometries. However, most current work that uses machine learning to speed up the solution process relies heavily on a fixed parameterization of the geometry, which cannot be changed after training. This severely limits the possibility of reusing a trained model across a variety of design problems. In this work, we propose a novel neural operator architecture which accepts boundary geometry, in the form of triangular meshes, as input and produces an approximate solution to a given PDE as output. Once trained, the model can be used to rapidly estimate the PDE solution over a new geometry, without the need for retraining or representation of the geometry to a pre-specified parameterization.

The use of non-Cartesian grids is a niche but important topic in sub-fields of the numerical sciences such as simulation and scientific visualization. However, non-Cartesian approaches are virtually unexplored in machine learning. This is likely due to the difficulties in the representation of data on non-Cartesian domains and the lack of support for standard machine learning operations on non-Cartesian data. This paper proposes a new data structure called the lattice tensor which generalizes traditional tensor spatio-temporal operations to lattice tensors, enabling the use of standard machine learning algorithms on non-Cartesian data. However, data need not reside on a non-Cartesian structure, we use non-Dyadic downsampling schemes to bring Cartesian data into a non-Cartesian space for further processing. We introduce a software library that implements the lattice tensor container (with some common machine learning operations), and demonstrate its effectiveness. Our method provides a general framework for machine learning on non-Cartesian domains, addressing the challenges mentioned above and filling a gap in the current literature.

Estimation and inference in statistics pose significant challenges when data are collected adaptively. Even in linear models, the Ordinary Least Squares (OLS) estimator may fail to exhibit asymptotic normality for single coordinate estimation and have inflated error. This issue is highlighted by a recent minimax lower bound, which shows that the error of estimating a single coordinate can be enlarged by a multiple of $\sqrt{d}$ when data are allowed to be arbitrarily adaptive, compared with the case when they are i.i.d. Our work explores this striking difference in estimation performance between utilizing i.i.d. and adaptive data. We investigate how the degree of adaptivity in data collection impacts the performance of estimating a low-dimensional parameter component in high-dimensional linear models. We identify conditions on the data collection mechanism under which the estimation error for a low-dimensional parameter component matches its counterpart in the i.i.d. setting, up to a factor that depends on the degree of adaptivity. We show that OLS or OLS on centered data can achieve this matching error. In addition, we propose a novel estimator for single coordinate inference via solving a Two-stage Adaptive Linear Estimating equation (TALE). Under a weaker form of adaptivity in data collection, we establish an asymptotic normality property of the proposed estimator.

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is persistent homology, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. A central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms. Existing approaches to this problem either ignore most of the multiparameter information to reduce to the one-parameter case or are heuristic and potentially unstable in the face of noise. In this article, we introduce a new general representation framework that leverages recent results on decompositions of multiparameter persistent homology. This framework is rich in information, fast to compute, and encompasses previous approaches. Moreover, we establish theoretical stability guarantees under this framework as well as efficient algorithms for practical computation, making this framework an applicable and versatile tool for analyzing geometric and point cloud data. We validate our stability results and algorithms with numerical experiments that demonstrate statistical convergence, prediction accuracy, and fast running times on several real data sets.

Computational cognitive models are a fundamental tool in behavioral neuroscience. They embody in software precise hypotheses about the cognitive mechanisms underlying a particular behavior. Constructing these models is typically a difficult iterative process that requires both inspiration from the literature and the creativity of an individual researcher. Here, we adopt an alternative approach to learn parsimonious cognitive models directly from data. We fit behavior data using a recurrent neural network that is penalized for carrying excess information between timesteps, leading to sparse, interpretable representations and dynamics. When fitting synthetic behavioral data from known cognitive models, our method recovers the underlying form of those models. When fit to choice data from rats performing a bandit task, our method recovers simple and interpretable models that make testable predictions about neural mechanisms.

Neural posterior estimation methods based on discrete normalizing flows have become established tools for simulation-based inference (SBI), but scaling them to high-dimensional problems can be challenging. Building on recent advances in generative modeling, we here present flow matching posterior estimation (FMPE), a technique for SBI using continuous normalizing flows. Like diffusion models, and in contrast to discrete flows, flow matching allows for unconstrained architectures, providing enhanced flexibility for complex data modalities. Flow matching, therefore, enables exact density evaluation, fast training, and seamless scalability to large architectures---making it ideal for SBI. We show that FMPE achieves competitive performance on an established SBI benchmark, and then demonstrate its improved scalability on a challenging scientific problem: for gravitational-wave inference, FMPE outperforms methods based on comparable discrete flows, reducing training time by 30\% with substantially improved accuracy. Our work underscores the potential of FMPE to enhance performance in challenging inference scenarios, thereby paving the way for more advanced applications to scientific problems.

Quantifying dependence between high-dimensional random variables is central to statistical learning and inference. Two classical methods are canonical correlation analysis (CCA), which identifies maximally correlated projected versions of the original variables, and Shannon's mutual information, which is a universal dependence measure that also captures high-order dependencies. However, CCA only accounts for linear dependence, which may be insufficient for certain applications, while mutual information is often infeasible to compute/estimate in high dimensions. This work proposes a middle ground in the form of a scalable information-theoretic generalization of CCA, termed max-sliced mutual information (mSMI). mSMI equals the maximal mutual information between low-dimensional projections of the high-dimensional variables, which reduces back to CCA in the Gaussian case. It enjoys the best of both worlds: capturing intricate dependencies in the data while being amenable to fast computation and scalable estimation from samples. We show that mSMI retains favorable structural properties of Shannon's mutual information, like variational forms and identification of independence. We then study statistical estimation of mSMI, propose an efficiently computable neural estimator, and couple it with formal non-asymptotic error bounds. We present experiments that demonstrate the utility of mSMI for several tasks, encompassing independence testing, multi-view representation learning, algorithmic fairness, and generative modeling. We observe that mSMI consistently outperforms competing methods with little-to-no computational overhead.

A popular perspective in Reinforcement learning (RL) casts the problem as probabilistic inference on a graphical model of the Markov decision process (MDP). The core object of study is the probability of each state-action pair being visited under the optimal policy. Previous approaches to approximate this quantity can be arbitrarily poor, leading to algorithms that do not implement genuine statistical inference and consequently do not perform well in challenging problems. In this work, we undertake a rigorous Bayesian treatment of the posterior probability of state-action optimality and clarify how it flows through the MDP. We first reveal that this quantity can indeed be used to generate a policy that explores efficiently, as measured by regret. Unfortunately, computing it is intractable, so we derive a new variational Bayesian approximation yielding a tractable convex optimization problem and establish that the resulting policy also explores efficiently. We call our approach VAPOR and show that it has strong connections to Thompson sampling, K-learning, and maximum entropy exploration. We conclude with some experiments demonstrating the performance advantage of a deep RL version of VAPOR.

Symbolic regression (SR) is a challenging task in machine learning that involves finding a mathematical expression for a function based on its values. Recent advancements in SR have demonstrated the effectiveness of pre-trained transformer-based models in generating equations as sequences, leveraging large-scale pre-training on synthetic datasets and offering notable advantages in terms of inference time over classical Genetic Programming (GP) methods. However, these models primarily rely on supervised pre-training goals borrowed from text generation and overlook equation discovery objectives like accuracy and complexity. To address this, we propose TPSR, a Transformer-based Planning strategy for Symbolic Regression that incorporates Monte Carlo Tree Search into the transformer decoding process. Unlike conventional decoding strategies, TPSR enables the integration of non-differentiable feedback, such as fitting accuracy and complexity, as external sources of knowledge into the transformer-based equation generation process. Extensive experiments on various datasets show that our approach outperforms state-of-the-art methods, enhancing the model's fitting-complexity trade-off, extrapolation abilities, and robustness to noise

Neural ordinary differential equations (NODEs) have been proven useful for learning non-linear dynamics of arbitrary trajectories. However, current NODE methods capture variations across trajectories only via the initial state value or by auto-regressive encoder updates. In this work, we introduce Modulated Neural ODEs (MoNODEs), a novel framework that sets apart dynamics states from underlying static factors of variation and improves the existing NODE methods. In particular, we introduce *time-invariant modulator variables* that are learned from the data. We incorporate our proposed framework into four existing NODE variants. We test MoNODE on oscillating systems, videos and human walking trajectories, where each trajectory has trajectory-specific modulation. Our framework consistently improves the existing model ability to generalize to new dynamic parameterizations and to perform far-horizon forecasting. In addition, we verify that the proposed modulator variables are informative of the true unknown factors of variation as measured by $R^2$ scores.

Simulation-Based Inference (SBI) is a common name for an emerging family of approaches that infer the model parameters when the likelihood is intractable. Existing SBI methods either approximate the likelihood, such as Approximate Bayesian Computation (ABC) or directly model the posterior, such as Sequential Neural Posterior Estimation (SNPE). While ABC is efficient on low-dimensional problems, on higher-dimensional tasks, it is generally outperformed by SNPE, which leverages function approximation. In this paper, we propose Pseudo-Likelihood Inference (PLI), a new method that brings neural approximation into ABC, making it competitive on challenging Bayesian system identification tasks. By utilizing integral probability metrics, we introduce a smooth likelihood kernel with an adaptive bandwidth that is updated based on information-theoretic trust regions. Thanks to this formulation, our method (i) allows for optimizing neural posteriors via gradient descent, (ii) does not rely on summary statistics, and (iii) enables multiple observations as input. In comparison to SNPE, it leads to improved performance when more data is available. The effectiveness of PLI is evaluated on four classical SBI benchmark tasks and on a highly dynamic physical system, showing particular advantages on stochastic simulations and multi-modal posterior landscapes.

Denoising Diffusion Probabilistic Models (DDPMs) provide the foundation for the recent breakthroughs in generative modeling. Their Markovian structure makes it difficult to define DDPMs with distributions other than Gaussian or discrete. In this paper, we introduce Star-Shaped DDPM (SS-DDPM). Its *star-shaped diffusion process* allows us to bypass the need to define the transition probabilities or compute posteriors. We establish duality between star-shaped and specific Markovian diffusions for the exponential family of distributions and derive efficient algorithms for training and sampling from SS-DDPMs. In the case of Gaussian distributions, SS-DDPM is equivalent to DDPM. However, SS-DDPMs provide a simple recipe for designing diffusion models with distributions such as Beta, von Mises–Fisher, Dirichlet, Wishart and others, which can be especially useful when data lies on a constrained manifold. We evaluate the model in different settings and find it competitive even on image data, where Beta SS-DDPM achieves results comparable to a Gaussian DDPM. Our implementation is available at https://github.com/andrey-okhotin/star-shaped

We present a novel perspective and algorithm for learning directed acyclic graphs (DAGs) from data generated by a linear structural equation model (SEM). First, we show that a linear SEM can be viewed as a linear transform that, in prior work, computes the data from a dense input vector of random valued root causes (as we will call them) associated with the nodes. Instead, we consider the case of (approximately) few root causes and also introduce noise in the measurement of the data. Intuitively, this means that the DAG data is produced by few data generating events whose effect percolates through the DAG. We prove identifiability in this new setting and show that the true DAG is the global minimizer of the $L^0$-norm of the vector of root causes. For data satisfying the few root causes assumption, we show superior performance compared to prior DAG learning methods.

Independent Component Analysis (ICA) aims to recover independent latent variables from observed mixtures thereof. Causal Representation Learning (CRL) aims instead to infer causally related (thus often statistically _dependent_) latent variables, together with the unknown graph encoding their causal relationships. We introduce an intermediate problem termed _Causal Component Analysis (CauCA)_. CauCA can be viewed as a generalization of ICA, modelling the causal dependence among the latent components, and as a special case of CRL. In contrast to CRL, it presupposes knowledge of the causal graph, focusing solely on learning the unmixing function and the causal mechanisms. Any impossibility results regarding the recovery of the ground truth in CauCA also apply for CRL, while possibility results may serve as a stepping stone for extensions to CRL. We characterize CauCA identifiability from multiple datasets generated through different types of interventions on the latent causal variables. As a corollary, this interventional perspective also leads to new identifiability results for nonlinear ICA—a special case of CauCA with an empty graph—requiring strictly fewer datasets than previous results. We introduce a likelihood-based approach using normalizing flows to estimate both the unmixing function and the causal mechanisms, and demonstrate its effectiveness through extensive synthetic experiments in the CauCA and ICA setting.

This work is concerned with the estimation problem of linear model when the sample size is extremely large and the data dimension can vary with the sample size. In this setting, the least square estimator based on the full data is not feasible with limited computational resources. Many existing methods for this problem are based on the sketching technique which uses the sketched data to perform least square estimation. We derive fine-grained lower bounds of the conditional mean squared error for sketching methods. For sampling methods, our lower bound provides an attainable optimal convergence rate. Our result implies that when the dimension is large, there is hardly a sampling method can have a faster convergence rate than the uniform sampling method. To achieve a better statistical performance, we propose a new sketching method based on data averaging. The proposed method reduces the original data to a few averaged observations. These averaged observations still satisfy the linear model and are used to estimate the regression coefficients. The asymptotic behavior of the proposed estimation procedure is studied. Our theoretical results show that the proposed method can achieve a faster convergence rate than the optimal convergence rate for sampling methods. Theoretical and numerical results show that the proposed estimator has good statistical performance as well as low computational cost.

Recently, studies on machine learning have focused on methods that use symmetry implicit in a specific manifold as an inductive bias. Grassmann manifolds provide the ability to handle fundamental shapes represented as shape spaces, enabling stable shape analysis. In this paper, we present a novel approach in which we establish the theoretical foundations for learning distributions on the Grassmann manifold via continuous normalization flows, with the explicit goal of generating stable shapes. Our approach facilitates more robust generation by effectively eliminating the influence of extraneous transformations, such as rotations and inversions, through learning and generating within a Grassmann manifold designed to accommodate the essential shape information of the object. The experimental results indicated that the proposed method could generate high-quality samples by capturing the data structure. Furthermore, the proposed method significantly outperformed state-of-the-art methods in terms of the log-likelihood or evidence lower bound. The results obtained are expected to stimulate further research in this field, leading to advances for stable shape generation and analysis.

The increasing availability of graph-structured data motivates the task of optimising over functions defined on the node set of graphs. Traditional graph search algorithms can be applied in this case, but they may be sample-inefficient and do not make use of information about the function values; on the other hand, Bayesian optimisation is a class of promising black-box solvers with superior sample efficiency, but it has scarcely been applied to such novel setups. To fill this gap, we propose a novel Bayesian optimisation framework that optimises over functions defined on generic, large-scale and potentially unknown graphs. Through the learning of suitable kernels on graphs, our framework has the advantage of adapting to the behaviour of the target function. The local modelling approach further guarantees the efficiency of our method. Extensive experiments on both synthetic and real-world graphs demonstrate the effectiveness of the proposed optimisation framework.

We propose a general class of sample based explanations of machine learning models, which we term generalized representers. To measure the effect of a training sample on a model's test prediction, generalized representers use two components: a global sample importance that quantifies the importance of the training point to the model and is invariant to test samples, and a local sample importance that measures similarity between the training sample and the test point with a kernel. A key contribution of the paper is to show that generalized representers are the only class of sample based explanations satisfying a natural set of axiomatic properties. We discuss approaches to extract global importances given a kernel, and also natural choices of kernels given modern non-linear models. As we show, many popular existing sample based explanations could be cast as generalized representers with particular choices of kernels and approaches to extract global importances. Additionally, we conduct empirical comparisons of different generalized representers on two image classification datasets.

Learning to accurately represent environmental uncertainty is crucial for adaptive and optimal behaviors in various cognitive tasks. However, it remains unclear how the human brain, constrained by finite cognitive resources, constructs an internal model from an infinite space of probability distributions. In this study, we explore how these learned distributions deviate from the ground truth, resulting in observable inconsistency in a novel structured density estimation task. During each trial, human participants were asked to form and report the latent probability distribution functions underlying sequentially presented independent observations. As the number of observations increased, the reported predictive density became closer to the ground truth. Nevertheless, we observed an intriguing inconsistency in human structure estimation, specifically a large error in the number of reported clusters. Such inconsistency is invariant to the scale of the distribution and persists across stimulus modalities. We modeled uncertainty learning as approximate Bayesian inference in a nonparametric mixture prior of distributions. Human reports were best explained under resource rationality embodied in a decaying tendency towards model expansion. Our study offers insights into human cognitive processes under uncertainty and lays the groundwork for further exploration of resource-rational representations in the brain under more complex tasks.

Although pairwise causal relations have been extensively studied in observational longitudinal analyses across many disciplines, incorporating knowledge of causal pairs into deep learning models for temporal event sequences remains largely unexplored. In this paper, we propose a novel approach for enhancing the performance of transformer-based models in multivariate event sequences by injecting pairwise qualitative causal knowledge such as `event Z amplifies future occurrences of event Y'. We establish a new framework for causal inference in temporal event sequences using a transformer architecture, providing a theoretical justification for our approach, and show how to obtain unbiased estimates of the proposed measure. Experimental results demonstrate that our approach outperforms several state-of-the-art models in terms of prediction accuracy by effectively leveraging knowledge about causal pairs. We also consider a unique application where we extract knowledge around sequences of societal events by generating them from a large language model, and demonstrate how a causal knowledge graph can help with event prediction in such sequences. Overall, our framework offers a practical means of improving the performance of transformer-based models in multivariate event sequences by explicitly exploiting pairwise causal information.

Bayesian neural networks often approximate the weight-posterior with a Gaussian distribution. However, practical posteriors are often, even locally, highly non-Gaussian, and empirical performance deteriorates. We propose a simple parametric approximate posterior that adapts to the shape of the true posterior through a Riemannian metric that is determined by the log-posterior gradient. We develop a Riemannian Laplace approximation where samples naturally fall into weight-regions with low negative log-posterior. We show that these samples can be drawn by solving a system of ordinary differential equations, which can be done efficiently by leveraging the structure of the Riemannian metric and automatic differentiation. Empirically, we demonstrate that our approach consistently improves over the conventional Laplace approximation across tasks. We further show that, unlike the conventional Laplace approximation, our method is not overly sensitive to the choice of prior, which alleviates a practical pitfall of current approaches.

Simulation-based inference (SBI) enables amortized Bayesian inference for simulators with implicit likelihoods. But when we are primarily interested in the quality of predictive simulations, or when the model cannot exactly reproduce the observed data (i.e., is misspecified), targeting the Bayesian posterior may be overly restrictive. Generalized Bayesian Inference (GBI) aims to robustify inference for (misspecified) simulator models, replacing the likelihood-function with a cost function that evaluates the goodness of parameters relative to data. However, GBI methods generally require running multiple simulations to estimate the cost function at each parameter value during inference, making the approach computationally infeasible for even moderately complex simulators. Here, we propose amortized cost estimation (ACE) for GBI to address this challenge: We train a neural network to approximate the cost function, which we define as the expected distance between simulations produced by a parameter and observed data. The trained network can then be used with MCMC to infer GBI posteriors for any observation without running additional simulations. We show that, on several benchmark tasks, ACE accurately predicts cost and provides predictive simulations that are closer to synthetic observations than other SBI methods, especially for misspecified simulators. Finally, we apply ACE to infer parameters of the Hodgkin-Huxley model given real intracellular recordings from the Allen Cell Types Database. ACE identifies better data-matching parameters while being an order of magnitude more simulation-efficient than a standard SBI method. In summary, ACE combines the strengths of SBI methods and GBI to perform robust and simulation-amortized inference for scientific simulators.

Several recent unsupervised learning methods use probabilistic approaches to solve combinatorial optimization (CO) problems based on the assumption of statistically independent solution variables. We demonstrate that this assumption imposes performance limitations in particular on difficult problem instances. Our results corroborate that an autoregressive approach which captures statistical dependencies among solution variables yields superior performance on many popular CO problems. We introduce Subgraph Tokenization in which the configuration of a set of solution variables is represented by a single token. This tokenization technique alleviates the drawback of the long sequential sampling procedure which is inherent to autoregressive methods without sacrificing expressivity. Importantly, we theoretically motivate an annealed entropy regularization and show empirically that it is essential for efficient and stable learning.

In this work, we describe a method that determines an exact map from a finite set of subgraph densities to the parameters of a stochastic block model (SBM) matching these densities. Given a number K of blocks, the subgraph densities of a finite number of stars and bistars uniquely determines a single element of the class of all degree-separated stochastic block models with K blocks. Our method makes it possible to translate estimates of these subgraph densities into model parameters, and hence to use subgraph densities directly for inference. The computational overhead is negligible; computing the translation map is polynomial in K, but independent of the graph size once the subgraph densities are given.

Manifold learning flows are a class of generative modelling techniques that assume a low-dimensional manifold description of the data. The embedding of such a manifold into the high-dimensional space of the data is achieved via learnable invertible transformations. Therefore, once the manifold is properly aligned via a reconstruction loss, the probability density is tractable on the manifold and maximum likelihood can be used to optimize the network parameters. Naturally, the lower-dimensional representation of the data requires an injective-mapping. Recent approaches were able to enforce that the density aligns with the modelled manifold, while efficiently calculating the density volume-change term when embedding to the higher-dimensional space. However, unless the injective-mapping is analytically predefined, the learned manifold is not necessarily an \emph{efficient representation} of the data. Namely, the latent dimensions of such models frequently learn an entangled intrinsic basis, with degenerate information being stored in each dimension. Alternatively, if a locally orthogonal and/or sparse basis is to be learned, here coined canonical intrinsic basis, it can serve in learning a more compact latent space representation. Toward this end, we propose a canonical manifold learning flow method, where a novel optimization objective enforces the transformation matrix to have few prominent and non-degenerate basis functions. We demonstrate that by minimizing the off-diagonal manifold metric elements $\ell_1$-norm, we can achieve such a basis, which is simultaneously sparse and/or orthogonal. Canonical manifold flow yields a more efficient use of the latent space, automatically generating fewer prominent and distinct dimensions to represent data, and consequently a better approximation of target distributions than other manifold flow methods in most experiments we conducted, resulting in lower FID scores.

Several recent methods for interpretability model feature interactions by looking at the Hessian of a neural network. This poses a challenge for ReLU networks, which are piecewise-linear and thus have a zero Hessian almost everywhere. We propose SmoothHess, a method of estimating second-order interactions through Stein's Lemma. In particular, we estimate the Hessian of the network convolved with a Gaussian through an efficient sampling algorithm, requiring only network gradient calls. SmoothHess is applied post-hoc, requires no modifications to the ReLU network architecture, and the extent of smoothing can be controlled explicitly. We provide a non-asymptotic bound on the sample complexity of our estimation procedure. We validate the superior ability of SmoothHess to capture interactions on benchmark datasets and a real-world medical spirometry dataset.

Flexibly quantifying both irreducible aleatoric and model-dependent epistemic uncertainties plays an important role for complex regression problems. While deep neural networks in principle can provide this flexibility and learn heteroscedastic aleatoric uncertainties through non-linear functions, recent works highlight that maximizing the log likelihood objective parameterized by mean and variance can lead to compromised mean fits since the gradient are scaled by the predictive variance, and propose adjustments in line with this premise. We instead propose to use the natural parametrization of the Gaussian, which has been shown to be more stable for heteroscedastic regression based on non-linear feature maps and Gaussian processes. Further, we emphasize the significance of principled regularization of the network parameters and prediction. We therefore propose an efficient Laplace approximation for heteroscedastic neural networks that allows automatic regularization through empirical Bayes and provides epistemic uncertainties, both of which improve generalization. We showcase on a range of regression problems—including a new heteroscedastic image regression benchmark—that our methods are scalable, improve over previous approaches for heteroscedastic regression, and provide epistemic uncertainty without requiring hyperparameter tuning.

Dosing models often use differential equations to model biological dynamics. Neural differential equations in particular can learn to predict the derivative of a process, which permits predictions at irregular points of time. However, this temporal flexibility often comes with a high sensitivity to noise, whereas medical problems often present high noise and limited data. Moreover, medical dosing models must generalize reliably over individual patients and changing treatment policies. To address these challenges, we introduce the Neural Eigen Stochastic Differential Equation algorithm (NESDE). NESDE provides individualized modeling (using a hypernetwork over patient-level parameters); generalization to new treatment policies (using decoupled control); tunable expressiveness according to the noise level (using piecewise linearity); and fast, continuous, closed-form prediction (using spectral representation). We demonstrate the robustness of NESDE in both synthetic and real medical problems, and use the learned dynamics to publish simulated medical gym environments.

This paper provides statistical sample complexity bounds for score-matching and its applications in causal discovery. We demonstrate that accurate estimation of the score function is achievable by training a standard deep ReLU neural network using stochastic gradient descent. We establish bounds on the error rate of recovering causal relationships using the score-matching-based causal discovery method of Rolland et al. [2022], assuming a sufficiently good estimation of the score function. Finally, we analyze the upper bound of score-matching estimation within the score-based generative modeling, which has been applied for causal discovery but is also of independent interest within the domain of generative models.

We study causal representation learning, the task of inferring latent causal variables and their causal relations from high-dimensional functions (“mixtures”) of the variables. Prior work relies on weak supervision, in the form of counterfactual pre- and post-intervention views or temporal structure; places restrictive assumptions, such as linearity, on the mixing function or latent causal model; or requires partial knowledge of the generative process, such as the causal graph or intervention targets. We instead consider the general setting in which both the causal model and the mixing function are nonparametric. The learning signal takes the form of multiple datasets, or environments, arising from unknown interventions in the underlying causal model. Our goal is to identify both the ground truth latents and their causal graph up to a set of ambiguities which we show to be irresolvable from interventional data. We study the fundamental setting of two causal variables and prove that the observational distribution and one perfect intervention per node suffice for identifiability, subject to a genericity condition. This condition rules out spurious solutions that involve fine-tuning of the intervened and observational distributions, mirroring similar conditions for nonlinear cause-effect inference. For an arbitrary number of variables, we show that at least one pair of distinct perfect interventional domains per node guarantees identifiability. Further, we demonstrate that the strengths of causal influences among the latent variables are preserved by all equivalent solutions, rendering the inferred representation appropriate for drawing causal conclusions from new data. Our study provides the first identifiability results for the general nonparametric setting with unknown interventions, and elucidates what is possible and impossible for causal representation learning without more direct supervision.

This paper proposes a novel strategy for estimating the heterogeneous treatment effect called the Fused and Accurate Shrinkage Tree ($\mathrm{FAST}$). Our approach utilizes both trial and observational data to improve the accuracy and robustness of the estimator. Inspired by the concept of shrinkage estimation in statistics, we develop an optimal weighting scheme and a corresponding estimator that balances the unbiased estimator based on the trial data with the potentially biased estimator based on the observational data. Specifically, combined with tree-based techniques, we introduce a new split criterion that utilizes both trial data and observational data to more accurately estimate the treatment effect. Furthermore, we confirm the consistency of our proposed tree-based estimator and demonstrate the effectiveness of our criterion in reducing prediction error through theoretical analysis. The advantageous finite sample performance of the $\mathrm{FAST}$ and its ensemble version over existing methods is demonstrated via simulations and real data analysis.

Bayesian optimization is a powerful method for optimizing black-box functions with limited function evaluations. Recent works have shown that optimization in a latent space through deep generative models such as variational autoencoders leads to effective and efficient Bayesian optimization for structured or discrete data. However, as the optimization does not take place in the input space, it leads to an inherent gap that results in potentially suboptimal solutions. To alleviate the discrepancy, we propose Correlated latent space Bayesian Optimization (CoBO), which focuses on learning correlated latent spaces characterized by a strong correlation between the distances in the latent space and the distances within the objective function. Specifically, our method introduces Lipschitz regularization, loss weighting, and trust region recoordination to minimize the inherent gap around the promising areas. We demonstrate the effectiveness of our approach on several optimization tasks in discrete data, such as molecule design and arithmetic expression fitting, and achieve high performance within a small budget.

Machine learning approaches for solving partial differential equations require learning mappings between function spaces. While convolutional or graph neural networks are constrained to discretized functions, neural operators present a promising milestone toward mapping functions directly. Despite impressive results they still face challenges with respect to the domain geometry and typically rely on some form of discretization. In order to alleviate such limitations, we present CORAL, a new method that leverages coordinate-based networks for solving PDEs on general geometries. CORAL is designed to remove constraints on the input mesh, making it applicable to any spatial sampling and geometry. Its ability extends to diverse problem domains, including PDE solving, spatio-temporal forecasting, and inverse problems like geometric design. CORAL demonstrates robust performance across multiple resolutions and performs well in both convex and non-convex domains, surpassing or performing on par with state-of-the-art models.

Markov decision processes (MDPs) often suffer from the sensitivity issue under model ambiguity. In recent years, robust MDPs have emerged as an effective framework to overcome this challenge. Distributionally robust MDPs extend the robust MDP framework by incorporating distributional information of the uncertain model parameters to alleviate the conservative nature of robust MDPs. This paper proposes a computationally efficient solution framework for solving distributionally robust MDPs with Wasserstein ambiguity sets. By exploiting the specific problem structure, the proposed framework decomposes the optimization problems associated with distributionally robust Bellman updates into smaller subproblems, which can be solved efficiently. The overall complexity of the proposed algorithm is quasi-linear in both the numbers of states and actions when the distance metric of the Wasserstein distance is chosen to be $L_1$, $L_2$, or $L_{\infty}$ norm, and so the computational cost of distributional robustness is substantially reduced. Our numerical experiments demonstrate that the proposed algorithms outperform other state-of-the-art solution methods.

Multi-fidelity fusion has become an important surrogate technique, which provides insights into expensive computer simulations and effectively improves decision-making, e.g., optimization, with less computational cost. Multi-fidelity fusion is much more computationally efficient compared to traditional single-fidelity surrogates. Despite the fast advancement of multi-fidelity fusion techniques, they lack a systematic framework to make use of the fidelity indicator, deal with high-dimensional and arbitrary data structure, and scale well to infinite-fidelity problems. In this work, we first generalize the popular autoregression (AR) to derive a novel linear fidelity differential equation (FiDE), paving the way to tractable infinite-fidelity fusion. We generalize FiDE to a high-dimensional system, which also provides a unifying framework to seemly bridge the gap between many multi- and single-fidelity GP-based models. We then propose ContinuAR, a rank-1 approximation solution to FiDEs, which is tractable to train, compatible with arbitrary multi-fidelity data structure, linearly scalable to the output dimension, and most importantly, delivers consistent SOTA performance with a significant margin over the baseline methods. Compared to the SOTA infinite-fidelity fusion, IFC, ContinuAR achieves up to 4x improvement in accuracy and 62,500x speedup in training time.

Normalizing flows are a class of deep generative models that are especially interesting for modeling probability distributions in physics, where the exact likelihood of flows allows reweighting to known target energy functions and computing unbiased observables. For instance, Boltzmann generators tackle the long-standing sampling problem in statistical physics by training flows to produce equilibrium samples of many-body systems such as small molecules and proteins. To build effective models for such systems, it is crucial to incorporate the symmetries of the target energy into the model, which can be achieved by equivariant continuous normalizing flows (CNFs). However, CNFs can be computationally expensive to train and generate samples from, which has hampered their scalability and practical application. In this paper, we introduce equivariant flow matching, a new training objective for equivariant CNFs that is based on the recently proposed optimal transport flow matching. Equivariant flow matching exploits the physical symmetries of the target energy for efficient, simulation-free training of equivariant CNFs. We demonstrate the effectiveness of flow matching on rotation and permutation invariant many-particle systems and a small molecule, alanine dipeptide, where for the first time we obtain a Boltzmann generator with significant sampling efficiency without relying on tailored internal coordinate featurization. Our results show that the equivariant flow matching objective yields flows with shorter integration paths, improved sampling efficiency, and higher scalability compared to existing methods.

Gaussian process regression is widely used because of its ability to provide well-calibrated uncertainty estimates and handle small or sparse datasets. However, it struggles with high-dimensional data. One possible way to scale this technique to higher dimensions is to leverage the implicit low-dimensional manifold upon which the data actually lies, as postulated by the manifold hypothesis. Prior work ordinarily requires the manifold structure to be explicitly provided though, i.e. given by a mesh or be known to be one of the well-known manifolds like the sphere. In contrast, in this paper we propose a Gaussian process regression technique capable of inferring implicit structure directly from data (labeled and unlabeled) in a fully differentiable way. For the resulting model, we discuss its convergence to the Matérn Gaussian process on the assumed manifold. Our technique scales up to hundreds of thousands of data points, and may improve the predictive performance and calibration of the standard Gaussian process regression in high-dimensional settings.

We propose a causal interpretation of self-attention in the Transformer neural network architecture. We interpret self-attention as a mechanism that estimates a structural equation model for a given input sequence of symbols (tokens). The structural equation model can be interpreted, in turn, as a causal structure over the input symbols under the specific context of the input sequence. Importantly, this interpretation remains valid in the presence of latent confounders. Following this interpretation, we estimate conditional independence relations between input symbols by calculating partial correlations between their corresponding representations in the deepest attention layer. This enables learning the causal structure over an input sequence using existing constraint-based algorithms. In this sense, existing pre-trained Transformers can be utilized for zero-shot causal-discovery. We demonstrate this method by providing causal explanations for the outcomes of Transformers in two tasks: sentiment classification (NLP) and recommendation.

Credal networks extend Bayesian networks to allow for imprecision in probability values. Marginal MAP is a widely applicable mixed inference task that identifies the most likely assignment for a subset of variables (called MAP variables). However, the task is extremely difficult to solve in credal networks particularly because the evaluation of each complete MAP assignment involves exact likelihood computations (combinatorial sums) over the vertices of a complex joint credal set representing the space of all possible marginal distributions of the MAP variables. In this paper, we explore Credal Marginal MAP inference and develop new exact methods based on variable elimination and depth-first search as well as several approximation schemes based on the mini-bucket partitioning and stochastic local search. An extensive empirical evaluation demonstrates the effectiveness of our new methods on random as well as real-world benchmark problems.

Deep neural networks (DNNs) have recently emerged as a powerful paradigm for solving Markovian optimal stopping problems. However, a ready extension of DNN-based methods to non-Markovian settings requires significant state and parameter space expansion, manifesting the curse of dimensionality. Further, efficient state-space transformations permitting Markovian approximations, such as those afforded by recurrent neural networks (RNNs), are either structurally infeasible or are confounded by the curse of non-Markovianity. Considering these issues, we introduce, for the first time, an optimal stopping policy gradient algorithm (OSPG) that can leverage RNNs effectively in non-Markovian settings by implicitly optimizing value functions without recursion, mitigating the curse of non-Markovianity. The OSPG algorithm is derived from an inference procedure on a novel Bayesian network representation of discrete-time non-Markovian optimal stopping trajectories and, as a consequence, yields an offline policy gradient algorithm that eliminates expensive Monte Carlo policy rollouts.

Interacting particle systems have proven highly successful in various machine learning tasks, including approximate Bayesian inference and neural network optimization. However, the analysis of these systems often relies on the simplifying assumption of the \emph{mean-field} limit, where particle numbers approach infinity and infinitesimal step sizes are used. In practice, discrete time steps, finite particle numbers, and complex integration schemes are employed, creating a theoretical gap between continuous-time and discrete-time processes. In this paper, we present a novel framework that establishes a precise connection between these discrete-time schemes and their corresponding mean-field limits in terms of convergence properties and asymptotic behavior. By adopting a dynamical system perspective, our framework seamlessly integrates various numerical schemes that are typically analyzed independently. For example, our framework provides a unified treatment of optimizing an infinite-width two-layer neural network and sampling via Stein Variational Gradient descent, which were previously studied in isolation.

Gradient-based sampling algorithms have demonstrated their effectiveness in text generation, especially in the context of controlled text generation. However, there exists a lack of theoretically grounded and principled approaches for this task. In this paper, we take an important step toward building a principled approach for sampling from language models with gradient-based methods. We use discrete distributions given by language models to define densities and develop an algorithm based on Hamiltonian Monte Carlo to sample from them. We name our gradient-based technique Structured Voronoi Sampling (SVS). In an experimental setup where the reference distribution is known, we show that the empirical distribution of SVS samples is closer to the reference distribution compared to alternative sampling schemes. Furthermore, in a controlled generation task, SVS is able to generate fluent and diverse samples while following the control targets significantly better than other methods.

While diffusion models can successfully generate data and make predictions, they are predominantly designed for static images. We propose an approach for training diffusion models for dynamics forecasting that leverages the temporal dynamics encoded in the data, directly coupling it with the diffusion steps in the network. We train a stochastic, time-conditioned interpolator and a backbone forecaster network that mimic the forward and reverse processes of conventional diffusion models, respectively. This design choice naturally encodes multi-step and long-range forecasting capabilities, allowing for highly flexible, continuous-time sampling trajectories and the ability to trade-off performance with accelerated sampling at inference time. In addition, the dynamics-informed diffusion process imposes a strong inductive bias, allowing for improved computational efficiency compared to traditional Gaussian noise-based diffusion models. Our approach performs competitively on probabilistic skill score metrics in complex dynamics forecasting of sea surface temperatures, Navier-Stokes flows, and spring mesh systems.

Policy gradient methods have become a standard for training reinforcement learning agents in a scalable and efficient manner. However, they do not account for transition uncertainty, whereas learning robust policies can be computationally expensive. In this paper, we introduce robust policy gradient (RPG), a policy-based method that efficiently solves rectangular robust Markov decision processes (MDPs). We provide a closed-form expression for the worst occupation measure. Incidentally, we find that the worst kernel is a rank-one perturbation of the nominal. Combining the worst occupation measure with a robust Q-value estimation yields an explicit form of the robust gradient. Our resulting RPG can be estimated from data with the same time complexity as its non-robust equivalent. Hence, it relieves the computational burden of convex optimization problems required for training robust policies by current policy gradient approaches.

Learning continuous-time point processes is essential to many discrete event forecasting tasks. However, integration poses a major challenge, particularly for spatiotemporal point processes (STPPs), as it involves calculating the likelihood through triple integrals over space and time. Existing methods for integrating STPP either assume a parametric form of the intensity function, which lacks flexibility; or approximating the intensity with Monte Carlo sampling, which introduces numerical errors. Recent work by Omi et al. proposes a dual network approach for efficient integration of flexible intensity function. However, their method only focuses on the 1D temporal point process. In this paper, we introduce a novel paradigm: `Auto-STPP` (Automatic Integration for Spatiotemporal Neural Point Processes) that extends the dual network approach to 3D STPP. While previous work provides a foundation, its direct extension overly restricts the intensity function and leads to computational challenges. In response, we introduce a decomposable parametrization for the integral network using ProdNet. This approach, leveraging the product of simplified univariate graphs, effectively sidesteps the computational complexities inherent in multivariate computational graphs. We prove the consistency of `Auto-STPP` and validate it on synthetic data and benchmark real-world datasets. `Auto-STPP` shows a significant advantage in recovering complex intensity functions from irregular spatiotemporal events, particularly when the intensity is sharply localized. Our code is open-source at https://github.com/Rose-STL-Lab/AutoSTPP.

Constraint-based causal discovery methods leverage conditional independence tests to infer causal relationships in a wide variety of applications. Just as the majority of machine learning methods, existing work focuses on studying $\textit{independent and identically distributed}$ data. However, it is known that even with infinite $i.i.d.\$ data, constraint-based methods can only identify causal structures up to broad Markov equivalence classes, posing a fundamental limitation for causal discovery. In this work, we observe that exchangeable data contains richer conditional independence structure than $i.i.d.\$ data, and show how the richer structure can be leveraged for causal discovery. We first present causal de Finetti theorems, which state that exchangeable distributions with certain non-trivial conditional independences can always be represented as $\textit{independent causal mechanism (ICM)}$ generative processes. We then present our main identifiability theorem, which shows that given data from an ICM generative process, its unique causal structure can be identified through performing conditional independence tests. We finally develop a causal discovery algorithm and demonstrate its applicability to inferring causal relationships from multi-environment data.

Knowledge graph (KG) reasoning utilizes two primary techniques, i.e., rule-based and KG-embedding based. The former provides precise inferences, but inferring via concrete rules is not scalable. The latter enables efficient reasoning at the cost of ambiguous inference accuracy. Neuro-symbolic reasoning seeks to amalgamate the advantages of both techniques. The crux of this approach is replacing the predicted existence of all possible triples (i.e., truth scores inferred from rules) with a suitable approximation grounded in embedding representations. However, constructing an effective approximation of all possible triples' truth scores is a challenging task, because it needs to balance the tradeoff between accuracy and efficiency, while compatible with both the rule-based and KG-embedding models. To this end, we proposed a differentiable framework - DiffLogic. Instead of directly approximating all possible triples, we design a tailored filter to adaptively select essential triples based on the dynamic rules and weights. The truth scores assessed by KG-embedding are continuous, so we employ a continuous Markov logic network named probabilistic soft logic (PSL). It employs the truth scores of essential triples to assess the overall agreement among rules, weights, and observed triples. PSL enables end-to-end differentiable optimization, so we can alternately update embedding and weighted rules. On benchmark datasets, we empirically show that DiffLogic surpasses baselines in both effectiveness and efficiency.

A common assumption in causal inference from observational data is that there is no hidden confounding. Yet it is, in general, impossible to verify the presence of hidden confounding factors from a single dataset. Under the assumption of independent causal mechanisms underlying the data-generating process, we demonstrate a way to detect unobserved confounders when having multiple observational datasets coming from different environments. We present a theory for testable conditional independencies that are only absent when there is hidden confounding and examine cases where we violate its assumptions: degenerate & dependent mechanisms, and faithfulness violations. Additionally, we propose a procedure to test these independencies and study its empirical finite-sample behavior using simulation studies and semi-synthetic data based on a real-world dataset. In most cases, the proposed procedure correctly predicts the presence of hidden confounding, particularly when the confounding bias is large.

The McKean-Vlasov equation (MVE) describes the collective behavior of particles subject to drift, diffusion, and mean-field interaction. In physical systems, the interaction term can be singular, i.e. it diverges when two particles collide. Notable examples of such interactions include the Coulomb interaction, fundamental in plasma physics, and the Biot-Savart interaction, present in the vorticity formulation of the 2D Navier-Stokes equation (NSE) in fluid dynamics. Solving MVEs that involve singular interaction kernels presents a significant challenge, especially when aiming to provide rigorous theoretical guarantees. In this work, we propose a novel approach based on the concept of entropy dissipation in the underlying system. We derive a potential function that effectively controls the KL divergence between a hypothesis solution and the ground truth. Building upon this theoretical foundation, we introduce the Entropy-dissipation Informed Neural Network (EINN) framework for solving MVEs. In EINN, we utilize neural networks (NN) to approximate the underlying velocity field and minimize the proposed potential function. By leveraging the expressive power of NNs, our approach offers a promising avenue for tackling the complexities associated with singular interactions. To assess the empirical performance of our method, we compare EINN with SOTA NN-based MVE solvers. The results demonstrate the effectiveness of our approach in solving MVEs across various example problems.

We propose a novel methodology that systematically analyzes ordinary differential equation (ODE) models for first-order optimization methods by converting the task of proving convergence rates into verifying the positive semidefiniteness of specific Hilbert-Schmidt integral operators. Our approach is based on the performance estimation problems (PEP) introduced by Drori and Teboulle. Unlike previous works on PEP, which rely on finite-dimensional linear algebra, we use tools from functional analysis. Using the proposed method, we establish convergence rates of various accelerated gradient flow models, some of which are new. As an immediate consequence of our framework, we show a correspondence between minimizing function values and minimizing gradient norms.

We study the computation of doubly regularized Wasserstein barycenters, a recently introduced family of entropic barycenters governed by inner and outer regularization strengths. Previous research has demonstrated that various regularization parameter choices unify several notions of entropy-penalized barycenters while also revealing new ones, including a special case of debiased barycenters. In this paper, we propose and analyze an algorithm for computing doubly regularized Wasserstein barycenters. Our procedure builds on damped Sinkhorn iterations followed by exact maximization/minimization steps and guarantees convergence for any choice of regularization parameters. An inexact variant of our algorithm, implementable using approximate Monte Carlo sampling, offers the first non-asymptotic convergence guarantees for approximating Wasserstein barycenters between discrete point clouds in the free-support/grid-free setting.

Unlike traditional statistical models depending on hand-specified priors, neural processes (NPs) have recently emerged as a class of powerful neural statistical models that combine the strengths of neural networks and stochastic processes. NPs can define a flexible class of stochastic processes well suited for highly non-trivial functions by encoding contextual knowledge into the function space. However, noisy context points introduce challenges to the algorithmic stability that small changes in training data may significantly change the models and yield lower generalization performance. In this paper, we provide theoretical guidelines for deriving stable solutions with high generalization by introducing the notion of algorithmic stability into NPs, which can be flexible to work with various NPs and achieves less biased approximation with theoretical guarantees. To illustrate the superiority of the proposed model, we perform experiments on both synthetic and real-world data, and the results demonstrate that our approach not only helps to achieve more accurate performance but also improves model robustness.

Additive Noise Models (ANMs) are a common model class for causal discovery from observational data. Due to a lack of real-world data for which an underlying ANM is known, ANMs with randomly sampled parameters are commonly used to simulate data for the evaluation of causal discovery algorithms. While some parameters may be fixed by explicit assumptions, fully specifying an ANM requires choosing all parameters. Reisach et al. (2021) show that, for many ANM parameter choices, sorting the variables by increasing variance yields an ordering close to a causal order and introduce ‘var-sortability’ to quantify this alignment. Since increasing variances may be unrealistic and cannot be exploited when data scales are arbitrary, ANM data are often rescaled to unit variance in causal discovery benchmarking. We show that synthetic ANM data are characterized by another pattern that is scale-invariant and thus persists even after standardization: the explainable fraction of a variable’s variance, as captured by the coefficient of determination $R^2$, tends to increase along the causal order. The result is high ‘$R^2$-sortability’, meaning that sorting the variables by increasing $R^2$ yields an ordering close to a causal order. We propose a computationally efficient baseline algorithm termed ‘$R^2$-SortnRegress’ that exploits high $R^2$-sortability and that can match and exceed the performance of established causal discovery algorithms. We show analytically that sufficiently high edge weights lead to a relative decrease of the noise contributions along causal chains, resulting in increasingly deterministic relationships and high $R^2$. We characterize $R^2$-sortability on synthetic data with different simulation parameters and find high values in common settings. Our findings reveal high $R^2$-sortability as an assumption about the data generating process relevant to causal discovery and implicit in many ANM sampling schemes. It should be made explicit, as its prevalence in real-world data is an open question. For causal discovery benchmarking, we provide implementations of $R^2$-sortability, the $R^2$-SortnRegress algorithm, and ANM simulation procedures in our library CausalDisco at https://causaldisco.github.io/CausalDisco/.

The aim of this paper is to make clear and precise the relationship between the Rubin causal model (RCM) and structural causal model (SCM) frameworks for causal inference. Adopting a neutral logical perspective, and drawing on previous work, we show what is required for an RCM to be representable by an SCM. A key result then shows that every RCM---including those that violate algebraic principles implied by the SCM framework---emerges as an abstraction of some representable RCM. Finally, we illustrate the power of this ameliorative perspective by pinpointing an important role for SCM principles in classic applications of RCMs; conversely, we offer a characterization of the algebraic constraints implied by a graph, helping to substantiate further comparisons between the two frameworks.

We have recently seen great progress in learning interpretable music representations, ranging from basic factors, such as pitch and timbre, to high-level concepts, such as chord and texture. However, most methods rely heavily on music domain knowledge. It remains an open question what general computational principles *give rise to* interpretable representations, especially low-dim factors that agree with human perception. In this study, we take inspiration from modern physics and use *physical symmetry* as a self-consistency constraint for the latent space. Specifically, it requires the prior model that characterises the dynamics of the latent states to be *equivariant* with respect to certain group transformations. We show that physical symmetry leads the model to learn a *linear* pitch factor from unlabelled monophonic music audio in a self-supervised fashion. In addition, the same methodology can be applied to computer vision, learning a 3D Cartesian space from videos of a simple moving object without labels. Furthermore, physical symmetry naturally leads to *representation augmentation*, a new technique which improves sample efficiency.

Many successful methods to learn dynamical systems from data have recently been introduced. However, ensuring that the inferred dynamics preserve known constraints, such as conservation laws or restrictions on the allowed system states, remains challenging. We propose stabilized neural differential equations (SNDEs), a method to enforce arbitrary manifold constraints for neural differential equations. Our approach is based on a stabilization term that, when added to the original dynamics, renders the constraint manifold provably asymptotically stable. Due to its simplicity, our method is compatible with all common neural differential equation (NDE) models and broadly applicable. In extensive empirical evaluations, we demonstrate that SNDEs outperform existing methods while broadening the types of constraints that can be incorporated into NDE training.

Neural Ordinary Differential Equations (NeuralODEs) present an attractive way to extract dynamical laws from time series data, as they bridge neural networks with the differential equation-based modeling paradigm of the physical sciences. However, these models often display long training times and suboptimal results, especially for longer duration data. While a common strategy in the literature imposes strong constraints to the NeuralODE architecture to inherently promote stable model dynamics, such methods are ill-suited for dynamics discovery as the unknown governing equation is not guaranteed to satisfy the assumed constraints. In this paper, we develop a new training method for NeuralODEs, based on synchronization and homotopy optimization, that does not require changes to the model architecture. We show that synchronizing the model dynamics and the training data tames the originally irregular loss landscape, which homotopy optimization can then leverage to enhance training. Through benchmark experiments, we demonstrate our method achieves competitive or better training loss while often requiring less than half the number of training epochs compared to other model-agnostic techniques. Furthermore, models trained with our method display better extrapolation capabilities, highlighting the effectiveness of our method.

When domain knowledge is limited and experimentation is restricted by ethical, financial, or time constraints, practitioners turn to observational causal discovery methods to recover the causal structure, exploiting the statistical properties of their data. Because causal discovery without further assumptions is an ill-posed problem, each algorithm comes with its own set of usually untestable assumptions, some of which are hard to meet in real datasets. Motivated by these considerations, this paper extensively benchmarks the empirical performance of recent causal discovery methods on observational _iid_ data generated under different background conditions, allowing for violations of the critical assumptions required by each selected approach. Our experimental findings show that score matching-based methods demonstrate surprising performance in the false positive and false negative rate of the inferred graph in these challenging scenarios, and we provide theoretical insights into their performance. This work is also the first effort to benchmark the stability of causal discovery algorithms with respect to the values of their hyperparameters. Finally, we hope this paper will set a new standard for the evaluation of causal discovery methods and can serve as an accessible entry point for practitioners interested in the field, highlighting the empirical implications of different algorithm choices.

Standard approaches for uncertainty quantification in deep learning and physics-informed learning have persistent limitations. Indicatively, strong assumptions regarding the data likelihood are required, the performance highly depends on the selection of priors, and the posterior can be sampled only approximately, which leads to poor approximations because of the associated computational cost. This paper introduces and studies confidence interval (CI) estimation for deterministic partial differential equations as a novel problem. That is, to propagate confidence, in the form of CIs, from data locations to the entire domain with probabilistic guarantees. We propose a method, termed Physics-Informed Confidence Propagation (PICProp), based on bi-level optimization to compute a valid CI without making heavy assumptions. We provide a theorem regarding the validity of our method, and computational experiments, where the focus is on physics-informed learning. Code is available at https://github.com/ShenQianli/PICProp.

Contemporary advances in the field of deep learning have embarked upon an exploration of the underlying geometric properties of data, thus encouraging the investigation of techniques that consider general manifolds, for example, hyperbolic or orthogonal neural networks. However, the optimization algorithms for training such geometric deep learning models still remain highly under-explored. In this paper, we introduce Riemannian SAM by generalizing conventional Euclidean SAM to Riemannian manifolds. We successfully formulate the sharpness-aware minimization on Riemannian manifolds, leading to one of a novel instantiation, Lorentz SAM. In addition, SAM variants proposed in previous studies such as Fisher SAM can be derived as special examples under our Riemannian SAM framework. We provide the convergence analysis of Riemannian SAM under a less aggressively decaying ascent learning rate than Euclidean SAM. Our analysis serves as a theoretically sound contribution encompassing a diverse range of manifolds, also providing the guarantees for SAM variants such as Fisher SAM, whose convergence analyses are absent. Lastly, we illustrate the superiority of Riemannian SAM in terms of generalization over previous Riemannian optimization algorithms through experiments on knowledge graph completion and machine translation tasks.

Constructing a directed cyclic graph (DCG) is challenged by both algorithmic difficulty and computational burden. Comparing multiple DCGs is even more difficult, compounded by the need of identifying variational causalities across graphs. We propose to unify multiple DCGs with a single structural model and develop a limited-information-based method to simultaneously construct multiple networks and infer their disparities, which can be visualized by appropriate correspondence analysis. The algorithm provides DCGs with robust non-asymptotic theoretical properties. It is designed with two sequential stages, each of which involves parallel computation tasks that are scalable to the network complexity. Taking advantage of high-performance clusters, our method makes it possible to evaluate the statistical significance of DCGs using the bootstrap method. We demonstrated the effectiveness of our method by applying it to synthetic and real datasets.

Tensor decompositions (TDs) serve as a powerful tool for analyzing multiway data. Traditional TDs incorporate prior knowledge about the data into the model, such as a directed generative process from latent factors to observations. In practice, selecting proper structural or distributional assumptions beforehand is crucial for obtaining a promising TD representation. However, since such prior knowledge is typically unavailable in real-world applications, choosing an appropriate TD model can be challenging. This paper aims to address this issue by introducing a flexible TD framework that discards the structural and distributional assumptions, in order to learn as much information from the data. Specifically, we construct a TD model that captures the joint probability of the data and latent tensor factors through a deep energy-based model (EBM). Neural networks are then employed to parameterize the joint energy function of tensor factors and tensor entries. The flexibility of EBM and neural networks enables the learning of underlying structures and distributions. In addition, by designing the energy function, our model unifies the learning process of different types of tensors, such as static tensors and dynamic tensors with time stamps. The resulting model presents a doubly intractable nature due to the presence of latent tensor factors and the unnormalized probability function. To efficiently train the model, we derive a variational upper bound of the conditional noise-contrastive estimation objective that learns the unnormalized joint probability by distinguishing data from conditional noises. We show advantages of our model on both synthetic and several real-world datasets.

Particle filters flexibly represent multiple posterior modes nonparametrically, via a collection of weighted samples, but have classically been applied to tracking problems with known dynamics and observation likelihoods. Such generative models may be inaccurate or unavailable for high-dimensional observations like images. We instead leverage training data to discriminatively learn particle-based representations of uncertainty in latent object states, conditioned on arbitrary observations via deep neural network encoders. While prior discriminative particle filters have used heuristic relaxations of discrete particle resampling, or biased learning by truncating gradients at resampling steps, we achieve unbiased and low-variance gradient estimates by representing posteriors as continuous mixture densities. Our theory and experiments expose dramatic failures of existing reparameterization-based estimators for mixture gradients, an issue we address via an importance-sampling gradient estimator. Unlike standard recurrent neural networks, our mixture density particle filter represents multimodal uncertainty in continuous latent states, improving accuracy and robustness. On a range of challenging tracking and robot localization problems, our approach achieves dramatic improvements in accuracy, will also showing much greater stability across multiple training runs.

Uncertainty quantification (UQ) is essential for creating trustworthy machine learning models. Recent years have seen a steep rise in UQ methods that can flag suspicious examples, however, it is often unclear what exactly these methods identify. In this work, we propose a framework for categorizing uncertain examples flagged by UQ methods. We introduce the confusion density matrix---a kernel-based approximation of the misclassification density---and use this to categorize suspicious examples identified by a given uncertainty method into three classes: out-of-distribution (OOD) examples, boundary (Bnd) examples, and examples in regions of high in-distribution misclassification (IDM). Through extensive experiments, we show that our framework provides a new and distinct perspective for assessing differences between uncertainty quantification methods, thereby forming a valuable assessment benchmark.

Fair Principal Component Analysis (PCA) is a problem setting where we aim to perform PCA while making the resulting representation fair in that the projected distributions, conditional on the sensitive attributes, match one another. However, existing approaches to fair PCA have two main problems: theoretically, there has been no statistical foundation of fair PCA in terms of learnability; practically, limited memory prevents us from using existing approaches, as they explicitly rely on full access to the entire data. On the theoretical side, we rigorously formulate fair PCA using a new notion called probably approximately fair and optimal (PAFO) learnability. On the practical side, motivated by recent advances in streaming algorithms for addressing memory limitation, we propose a new setting called fair streaming PCA along with a memory-efficient algorithm, fair noisy power method (FNPM). We then provide its statistical guarantee in terms of PAFO-learnability, which is the first of its kind in fair PCA literature. We verify our algorithm in the CelebA dataset without any pre-processing; while the existing approaches are inapplicable due to memory limitations, by turning it into a streaming setting, we show that our algorithm performs fair PCA efficiently and effectively.

Causality-based recommendation systems focus on the causal effects of user-item interactions resulting from item exposure (i.e., which items are recommended or exposed to the user), as opposed to conventional correlation-based recommendation. They are gaining popularity due to their multi-sided benefits to users, sellers and platforms alike. However, existing causality-based recommendation methods require additional input in the form of exposure data and/or propensity scores (i.e., the probability of exposure) for training. Such data, crucial for modeling causality in recommendation, are often not available in real-world situations due to technical or privacy constraints. In this paper, we bridge the gap by proposing a new framework, called Propensity Estimation for Causality-based Recommendation (PropCare). It can estimate the propensity and exposure from a more practical setup, where only interaction data are available *without* any ground truth on exposure or propensity in training and inference. We demonstrate that, by relating the pairwise characteristics between propensity and item popularity, PropCare enables competitive causality-based recommendation given only the conventional interaction data. We further present a theoretical analysis on the bias of the causal effect under our model estimation. Finally, we empirically evaluate PropCare through both quantitative and qualitative experiments.

Estimating individual treatment effects from observational data is challenging due to treatment selection bias. Prevalent methods mainly mitigate this issue by aligning different treatment groups in the latent space, the core of which is the calculation of distribution discrepancy. However, two issues that are often overlooked can render these methods invalid: (1) mini-batch sampling effects (MSE), where the calculated discrepancy is erroneous in non-ideal mini-batches with outcome imbalance and outliers; (2) unobserved confounder effects (UCE), where the unobserved confounders are not considered in the discrepancy calculation. Both of these issues invalidate the calculated discrepancy, mislead the training of estimators, and thus impede the handling of treatment selection bias. To tackle these issues, we propose Entire Space CounterFactual Regression (ESCFR), which is a new take on optimal transport technology in the context of causality. Specifically, based on the canonical optimal transport framework, we propose a relaxed mass-preserving regularizer to address the MSE issue and design a proximal factual outcome regularizer to handle the UCE issue. Extensive experiments demonstrate that ESCFR estimates distribution discrepancy accurately, handles the treatment selection bias effectively, and outperforms prevalent competitors significantly.

A Bayesian pseudocoreset is a compact synthetic dataset summarizing essential information of a large-scale dataset and thus can be used as a proxy dataset for scalable Bayesian inference. Typically, a Bayesian pseudocoreset is constructed by minimizing a divergence measure between the posterior conditioning on the pseudocoreset and the posterior conditioning on the full dataset. However, evaluating the divergence can be challenging, particularly for the models like deep neural networks having high-dimensional parameters. In this paper, we propose a novel Bayesian pseudocoreset construction method that operates on a function space. Unlike previous methods, which construct and match the coreset and full data posteriors in the space of model parameters (weights), our method constructs variational approximations to the coreset posterior on a function space and matches it to the full data posterior in the function space. By working directly on the function space, our method could bypass several challenges that may arise when working on a weight space, including limited scalability and multi-modality issue. Through various experiments, we demonstrate that the Bayesian pseudocoresets constructed from our method enjoys enhanced uncertainty quantification and better robustness across various model architectures.

This paper presents a framework for computing the Gromov-Wasserstein problem between two sets of points in low dimensional spaces, where the discrepancy is the squared Euclidean norm. The Gromov-Wasserstein problem is a generalization of the optimal transport problem that finds the assignment between two sets preserving pairwise distances as much as possible. This can be used to quantify the similarity between two formations or shapes, a common problem in AI and machine learning. The problem can be formulated as a Quadratic Assignment Problem (QAP), which is in general computationally intractable even for small problems. Our framework addresses this challenge by reformulating the QAP as an optimization problem with a low-dimensional domain, leveraging the fact that the problem can be expressed as a concave quadratic optimization problem with low rank. The method scales well with the number of points, and it can be used to find the global solution for large-scale problems with thousands of points. We compare the computational complexity of our approach with state-of-the-art methods on synthetic problems and apply it to a near-symmetrical problem which is of particular interest in computational biology.

By composing graphical models with deep learning architectures, we learn generative models with the strengths of both frameworks. The structured variational autoencoder (SVAE) inherits structure and interpretability from graphical models, and flexible likelihoods for high-dimensional data from deep learning, but poses substantial optimization challenges. We propose novel algorithms for learning SVAEs, and are the first to demonstrate the SVAE's ability to handle multimodal uncertainty when data is missing by incorporating discrete latent variables. Our memory-efficient implicit differentiation scheme makes the SVAE tractable to learn via gradient descent, while demonstrating robustness to incomplete optimization. To more rapidly learn accurate graphical model parameters, we derive a method for computing natural gradients without manual derivations, which avoids biases found in prior work. These optimization innovations enable the first comparisons of the SVAE to state-of-the-art time series models, where the SVAE performs competitively while learning interpretable and structured discrete data representations.

We propose the geometry-informed neural operator (GINO), a highly efficient approach to learning the solution operator of large-scale partial differential equations with varying geometries. GINO uses a signed distance function (SDF) representation of the input shape and neural operators based on graph and Fourier architectures to learn the solution operator. The graph neural operator handles irregular grids and transforms them into and from regular latent grids on which Fourier neural operator can be efficiently applied. We provide an efficient implementation of GINO using an optimized hashing approach, which allows efficient learning in a shared, compressed latent space with reduced computation and memory costs. GINO is discretization-invariant, meaning the trained model can be applied to arbitrary discretizations of the continuous domain and applies to any shape or resolution. To empirically validate the performance of our method on large-scale simulation, we generate the industry-standard aerodynamics dataset of 3D vehicle geometries with Reynolds numbers as high as five million. For this large-scale 3D fluid simulation, numerical methods are expensive to compute surface pressure. We successfully trained GINO to predict the pressure on car surfaces using only five hundred data points. The cost-accuracy experiments show a 26,000x speed-up compared to optimized GPU-based computational fluid dynamics (CFD) simulators on computing the drag coefficient. When tested on new combinations of geometries and boundary conditions (inlet velocities), GINO obtains a one-fourth reduction in error rate compared to deep neural network approaches.

The evaluation of generative models has received significant attention in the machine learning community. When applied to a multi-modal distribution which is common among image datasets, an intuitive evaluation criterion is the number of modes captured by the generative model. While several scores have been proposed to evaluate the quality and diversity of a model's generated data, the correspondence between existing scores and the number of modes in the distribution is unclear. In this work, we propose an information-theoretic diversity evaluation method for multi-modal underlying distributions. We utilize the R\'enyi Kernel Entropy (RKE) as an evaluation score based on quantum information theory to measure the number of modes in generated samples. To interpret the proposed evaluation method, we show that the RKE score can output the number of modes of a mixture of sub-Gaussian components. We also prove estimation error bounds for estimating the RKE score from limited data, suggesting a fast convergence of the empirical RKE score to the score for the underlying data distribution. Utilizing the RKE score, we conduct an extensive evaluation of state-of-the-art generative models over standard image datasets. The numerical results indicate that while the recent algorithms for training generative models manage to improve the mode-based diversity over the earlier architectures, they remain incapable of capturing the full diversity of real data. Our empirical results provide a ranking of widely-used generative models based on the RKE score of their generated samples.

Gaussian mixture models (GMMs) are fundamental to machine learning due to their flexibility as approximating densities. However, uncertainty quantification of GMMs remains a challenge as differential entropy lacks a closed form. This paper explores polynomial approximations, specifically Taylor and Legendre, to the GMM entropy from a theoretical and practical perspective. We provide new analysis of a widely used approach due to Huber et al.(2008) and show that the series diverges under simple conditions. Motivated by this divergence we provide a novel Taylor series that is provably convergent to the true entropy of any GMM. We demonstrate a method for selecting a center such that the series converges from below, providing a lower bound on GMM entropy. Furthermore, we demonstrate that orthogonal polynomial series result in more accurate polynomial approximations. Experimental validation supports our theoretical results while showing that our method is comparable in computation to Huber et al. We also show that in application, the use of these polynomial approximations, such as in Nonparametric Variational Inference by Gershamn et al. (2012), rely on the convergence of the methods in computing accurate approximations. This work contributes useful analysis to existing methods while introducing a novel approximation supported by firm theoretical guarantees.

Riemannian diffusion models draw inspiration from standard Euclidean space diffusion models to learn distributions on general manifolds. Unfortunately, the additional geometric complexity renders the diffusion transition term inexpressible in closed form, so prior methods resort to imprecise approximations of the score matching training objective that degrade performance and preclude applications in high dimensions. In this work, we reexamine these approximations and propose several practical improvements. Our key observation is that most relevant manifolds are symmetric spaces, which are much more amenable to computation. By leveraging and combining various ans\"{a}tze, we can quickly compute relevant quantities to high precision. On low dimensional datasets, our correction produces a noticeable improvement and is competitive with other techniques. Additionally, we show that our method enables us to scale to high dimensional tasks on nontrivial manifolds, including $SU(n)$ lattices in the context of lattice quantum chromodynamics (QCD). Finally, we apply our models to contrastively learned hyperspherical embeddings, curbing the representation collapse problem in the projection head and closing the gap between theory and practice.

This paper addresses the problem of nearly optimal Vapnik--Chervonenkis dimension (VC-dimension) and pseudo-dimension estimations of the derivative functions of deep neural networks (DNNs). Two important applications of these estimations include: 1) Establishing a nearly tight approximation result of DNNs in the Sobolev space; 2) Characterizing the generalization error of machine learning methods with loss functions involving function derivatives. This theoretical investigation fills the gap of learning error estimations for a wide range of physics-informed machine learning models and applications including generative models, solving partial differential equations, operator learning, network compression, distillation, regularization, etc.

Bases have become an integral part of modern deep learning-based models for time series forecasting due to their ability to act as feature extractors or future references. To be effective, a basis must be tailored to the specific set of time series data and exhibit distinct correlation with each time series within the set. However, current state-of-the-art methods are limited in their ability to satisfy both of these requirements simultaneously. To address this challenge, we propose BasisFormer, an end-to-end time series forecasting architecture that leverages learnable and interpretable bases. This architecture comprises three components: First, we acquire bases through adaptive self-supervised learning, which treats the historical and future sections of the time series as two distinct views and employs contrastive learning. Next, we design a Coef module that calculates the similarity coefficients between the time series and bases in the historical view via bidirectional cross-attention. Finally, we present a Forecast module that selects and consolidates the bases in the future view based on the similarity coefficients, resulting in accurate future predictions. Through extensive experiments on six datasets, we demonstrate that BasisFormer outperforms previous state-of-the-art methods by 11.04% and 15.78% respectively for univariate and multivariate forecasting tasks. Code is available at: https://github.com/nzl5116190/Basisformer.

The design and analysis of randomized experiments is fundamental to many areas, from the physical and social sciences to industrial settings. Regression adjustment is a popular technique to reduce the variance of estimates obtained from experiments, by utilizing information contained in auxiliary covariates. While there is a large literature within the statistics community studying various approaches to regression adjustment and their asymptotic properties, little focus has been given to approaches in the finite population setting with non-asymptotic accuracy bounds. Further, prior work typically assumes that an entire population is exposed to an experiment, whereas practitioners often seek to minimize the number of subjects exposed to an experiment, for ethical and pragmatic reasons. In this work, we study the problems of estimating the sample mean, individual treatment effects, and average treatment effect with regression adjustment. We propose approaches that use techniques from randomized numerical linear algebra to sample a subset of the population on which to perform an experiment. We give non-asymptotic accuracy bounds for our methods and demonstrate that they compare favorably with prior approaches.

We introduce a data-driven learning framework that assimilates two powerful ideas: ideal large eddy simulation (LES) from turbulence closure modeling and neural stochastic differential equations (SDE) for stochastic modeling. The ideal LES models the LES flow by treating each full-order trajectory as a random realization of the underlying dynamics, as such, the effect of small-scales is marginalized to obtain the deterministic evolution of the LES state. However, ideal LES is analytically intractable. In our work, we use a latent neural SDE to model the evolution of the stochastic process and an encoder-decoder pair for transforming between the latent space and the desired ideal flow field. This stands in sharp contrast to other types of neural parameterization of closure models where each trajectory is treated as a deterministic realization of the dynamics. We show the effectiveness of our approach (niLES – neural ideal LES) on two challenging chaotic dynamical systems: Kolmogorov flow at a Reynolds number of 20,000 and flow past a cylinder at Reynolds number 500. Compared to competing methods, our method can handle non-uniform geometries using unstructured meshes seamlessly. In particular, niLES leads to trajectories with more accurate statistics and enhances stability, particularly for long-horizon rollouts. (Source codes and datasets will be made publicly available.)

Sequential data collection has emerged as a widely adopted technique for enhancing the efficiency of data gathering processes. Despite its advantages, such data collection mechanism often introduces complexities to the statistical inference procedure. For instance, the ordinary least squares (OLS) estimator in an adaptive linear regression model can exhibit non-normal asymptotic behavior, posing challenges for accurate inference and interpretation. In this paper, we propose a general method for constructing debiased estimator which remedies this issue. It makes use of the idea of adaptive linear estimating equations, and we establish theoretical guarantees of asymptotic normality, supplemented by discussions on achieving near-optimal asymptotic variance. A salient feature of our estimator is that in the context of multi-armed bandits, our estimator retains the non-asymptotic performance of the least square estimator while obtaining asymptotic normality property. Consequently, this work helps connect two fruitful paradigms of adaptive inference: a) non-asymptotic inference using concentration inequalities and b) asymptotic inference via asymptotic normality.

We propose a new method for separating superimposed sources using diffusion-based generative models. Our method relies only on separately trained statistical priors of independent sources to establish a new objective function guided by $\textit{maximum a posteriori}$ estimation with an $\textit{$\alpha$-posterior}$, across multiple levels of Gaussian smoothing. Motivated by applications in radio-frequency (RF) systems, we are interested in sources with underlying discrete nature and the recovery of encoded bits from a signal of interest, as measured by the bit error rate (BER). Experimental results with RF mixtures demonstrate that our method results in a BER reduction of 95\% over classical and existing learning-based methods. Our analysis demonstrates that our proposed method yields solutions that asymptotically approach the modes of an underlying discrete distribution. Furthermore, our method can be viewed as a multi-source extension to the recently proposed score distillation sampling scheme, shedding additional light on its use beyond conditional sampling. The project webpage is available at https://alpha-rgs.github.io.

Human learners have ability to adopt appropriate learning approaches depending on constraints such as prior on the hypothesis, urgency of decision, and drift of the environment. However, existing learning models are typically considered individually rather than in relation to one and other. To build agents that have the ability to move between different modes of learning over time, it is important to understand how learning models are related as points in a broader space of possibilities. We introduce a mathematical framework, Generalized Belief Transport (GBT), that unifies and generalizes prior models, including Bayesian inference, cooperative communication and classification, as parameterizations of three learning constraints within Unbalanced Optimal Transport (UOT). We visualize the space of learning models encoded by GBT as a cube which includes classic learning models as special points. We derive critical properties of this parameterized space including proving continuity and differentiability which is the basis for model interpolation, and study limiting behavior of the parameters, which allows attaching learning models on the boundaries. Moreover, we investigate the long-run behavior of GBT, explore convergence properties of models in GBT mathematical and computationally, document the ability to learn in the presence of distribution drift, and formulate conjectures about general behavior. We conclude with open questions and implications for more unified models of learning.

We study the problems of sequential nonparametric two-sample and independence testing. Sequential tests process data online and allow using observed data to decide whether to stop and reject the null hypothesis or to collect more data, while maintaining type I error control. We build upon the principle of (nonparametric) testing by betting, where a gambler places bets on future observations and their wealth measures evidence against the null hypothesis. While recently developed kernel-based betting strategies often work well on simple distributions, selecting a suitable kernel for high-dimensional or structured data, such as images, is often nontrivial. To address this drawback, we design prediction-based betting strategies that rely on the following fact: if a sequentially updated predictor starts to consistently determine (a) which distribution an instance is drawn from, or (b) whether an instance is drawn from the joint distribution or the product of the marginal distributions (the latter produced by external randomization), it provides evidence against the two-sample or independence nulls respectively. We empirically demonstrate the superiority of our tests over kernel-based approaches under structured settings. Our tests can be applied beyond the case of independent and identically distributed data, remaining valid and powerful even when the data distribution drifts over time.

The signaling capacity of a neural population depends on the scale and orientation of its covariance across trials. Estimating this "noise" covariance is challenging and is thought to require a large number of stereotyped trials. New approaches are therefore needed to interrogate the structure of neural noise across rich, naturalistic behaviors and sensory experiences, with few trials per condition. Here, we exploit the fact that conditions are smoothly parameterized in many experiments and leverage Wishart process models to pool statistical power from trials in neighboring conditions. We demonstrate that these models perform favorably on experimental data from the mouse visual cortex and monkey motor cortex relative to standard covariance estimators. Moreover, they produce smooth estimates of covariance as a function of stimulus parameters, enabling estimates of noise correlations in entirely unseen conditions as well as continuous estimates of Fisher information—a commonly used measure of signal fidelity. Together, our results suggest that Wishart processes are broadly applicable tools for quantification and uncertainty estimation of noise correlations in trial-limited regimes, paving the way toward understanding the role of noise in complex neural computations and behavior.

Off-policy learning, referring to the procedure of policy optimization with access only to logged feedback data, has shown importance in various important real-world applications, such as search engines and recommender systems. While the ground-truth logging policy is usually unknown, previous work simply takes its estimated value for the off-policy learning, ignoring the negative impact from both high bias and high variance resulted from such an estimator. And these impact is often magnified on samples with small and inaccurately estimated logging probabilities. The contribution of this work is to explicitly model the uncertainty in the estimated logging policy, and propose an Uncertainty-aware Inverse Propensity Score estimator (UIPS) for improved off-policy learning, with a theoretical convergence guarantee. Experiment results on the synthetic and real-world recommendation datasets demonstrate that UIPS significantly improves the quality of the discovered policy, when compared against an extensive list of state-of-the-art baselines.

One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes and their products that control gene expression and cellular function. We can treat this as a causal discovery problem but with two non-standard challenges: (1) regulatory networks are inherently cyclic so we should not model a GRN as a directed acyclic graph (DAG), and (2) observations have significant measurement noise so for typical sample sizes, there will always be a large equivalence class of graphs that are likely given the data, and we want methods that capture this uncertainty. Existing methods either focus on challenge (1), identifying cyclic structure from dynamics, or on challenge (2) learning complex Bayesian posteriors over directed acyclic graphs, but not both. In this paper we leverage the fact that it is possible to estimate the ``velocity'' of the expression of a gene with RNA velocity techniques to develop an approach that addresses both challenges. Because we have access to velocity information, we can treat the Bayesian structure learning problem as a problem of sparse identification of a dynamical system, capturing cyclic feedback loops through time. We leverage Generative Flow Networks (GFlowNets) to estimate the posterior distribution over the combinatorial space of possible sparse dependencies. Our results indicate that our method learns posteriors that better encapsulate the distributions of cyclic structures compared to counterpart state-of-the-art Bayesian structure learning approaches.

Diffusion models have been successful on a range of conditional generation tasks including molecular design and text-to-image generation. However, these achievements have primarily depended on task-specific conditional training or error-prone heuristic approximations. Ideally, a conditional generation method should provide exact samples for a broad range of conditional distributions without requiring taskspecific training. To this end, we introduce the Twisted Diffusion Sampler, or TDS. TDS is a sequential Monte Carlo (SMC) algorithm that targets the conditional distributions of diffusion models. The main idea is to use twisting, an SMC technique that enjoys good computational efficiency, to incorporate heuristic approximations without compromising asymptotic exactness. We first find in simulation and in conditional image generation tasks that TDS provides a computational statistical trade-off, yielding more accurate approximations with many particles but with empirical improvements over heuristics with as few as two particles. We then turn to motif-scaffolding, a core task in protein design, using a TDS extension to Riemannian diffusion models; on benchmark test cases, TDS allows flexible conditioning criteria and often outperforms the state-of-the-art, conditionally trained model.

Online updating of time series forecasting models aims to address the concept drifting problem by efficiently updating forecasting models based on streaming data. Many algorithms are designed for online time series forecasting, with some exploiting cross-variable dependency while others assume independence among variables. Given every data assumption has its own pros and cons in online time series modeling, we propose **On**line **e**nsembling **Net**work (**OneNet**). It dynamically updates and combines two models, with one focusing on modeling the dependency across the time dimension and the other on cross-variate dependency. Our method incorporates a reinforcement learning-based approach into the traditional online convex programming framework, allowing for the linear combination of the two models with dynamically adjusted weights. OneNet addresses the main shortcoming of classical online learning methods that tend to be slow in adapting to the concept drift. Empirical results show that OneNet reduces online forecasting error by more than $\mathbf{50}\\%$ compared to the State-Of-The-Art (SOTA) method.

In real applications, interaction between machine learning models and domain experts is critical; however, the classical machine learning paradigm that usually produces only a single model does not facilitate such interaction. Approximating and exploring the Rashomon set, i.e., the set of all near-optimal models, addresses this practical challenge by providing the user with a searchable space containing a diverse set of models from which domain experts can choose. We present algorithms to efficiently and accurately approximate the Rashomon set of sparse, generalized additive models with ellipsoids for fixed support sets and use these ellipsoids to approximate Rashomon sets for many different support sets. The approximated Rashomon set serves as a cornerstone to solve practical challenges such as (1) studying the variable importance for the model class; (2) finding models under user-specified constraints (monotonicity, direct editing); and (3) investigating sudden changes in the shape functions. Experiments demonstrate the fidelity of the approximated Rashomon set and its effectiveness in solving practical challenges.

We study the problem of uncertainty quantification for time series prediction, with the goal of providing easy-to-use algorithms with formal guarantees. The algorithms we present build upon ideas from conformal prediction and control theory, are able to prospectively model conformal scores in an online setting, and adapt to the presence of systematic errors due to seasonality, trends, and general distribution shifts. Our theory both simplifies and strengthens existing analyses in online conformal prediction. Experiments on 4-week-ahead forecasting of statewide COVID-19 death counts in the U.S. show an improvement in coverage over the ensemble forecaster used in official CDC communications. We also run experiments on predicting electricity demand, market returns, and temperature using autoregressive, Theta, Prophet, and Transformer models. We provide an extendable codebase for testing our methods and for the integration of new algorithms, data sets, and forecasting rules at [this link](http://github.com/aangelopoulos/conformal-time-series).

Chaotic systems make long-horizon forecasts difficult because small perturbations in initial conditions cause trajectories to diverge at an exponential rate. In this setting, neural operators trained to minimize squared error losses, while capable of accurate short-term forecasts, often fail to reproduce statistical or structural properties of the dynamics over longer time horizons and can yield degenerate results. In this paper, we propose an alternative framework designed to preserve invariant measures of chaotic attractors that characterize the time-invariant statistical properties of the dynamics. Specifically, in the multi-environment setting (where each sample trajectory is governed by slightly different dynamics), we consider two novel approaches to training with noisy data. First, we propose a loss based on the optimal transport distance between the observed dynamics and the neural operator outputs. This approach requires expert knowledge of the underlying physics to determine what statistical features should be included in the optimal transport loss. Second, we show that a contrastive learning framework, which does not require any specialized prior knowledge, can preserve statistical properties of the dynamics nearly as well as the optimal transport approach. On a variety of chaotic systems, our method is shown empirically to preserve invariant measures of chaotic attractors.

Understanding which concepts models can and cannot represent has been fundamental to many tasks: from effective and responsible use of models to detecting out of distribution data. We introduce Gaussian process probes (GPP), a unified and simple framework for probing and measuring uncertainty about concepts represented by models. As a Bayesian extension of linear probing methods, GPP asks what kind of distribution over classifiers (of concepts) is induced by the model. This distribution can be used to measure both what the model represents and how confident the probe is about what the model represents. GPP can be applied to any pre-trained model with vector representations of inputs (e.g., activations). It does not require access to training data, gradients, or the architecture. We validate GPP on datasets containing both synthetic and real images. Our experiments show it can (1) probe a model's representations of concepts even with a very small number of examples, (2) accurately measure both epistemic uncertainty (how confident the probe is) and aleatory uncertainty (how fuzzy the concepts are to the model), and (3) detect out of distribution data using those uncertainty measures as well as classic methods do. By using Gaussian processes to expand what probing can offer, GPP provides a data-efficient, versatile and uncertainty-aware tool for understanding and evaluating the capabilities of machine learning models.

We introduce GAUCHE, an open-source library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to molecular representations, however, necessitates kernels defined over structured inputs such as graphs, strings and bit vectors. By providing such kernels in a modular, robust and easy-to-use framework, we seek to enable expert chemists and materials scientists to make use of state-of-the-art black-box optimization techniques. Motivated by scenarios frequently encountered in practice, we showcase applications for GAUCHE in molecular discovery, chemical reaction optimisation and protein design. The codebase is made available at https://github.com/leojklarner/gauche.

We establish conditions under which latent causal graphs are nonparametrically identifiable and can be reconstructed from unknown interventions in the latent space. Our primary focus is the identification of the latent structure in measurement models without parametric assumptions such as linearity or Gaussianity. Moreover, we do not assume the number of hidden variables is known, and we show that at most one unknown intervention per hidden variable is needed. This extends a recent line of work on learning causal representations from observations and interventions. The proofs are constructive and introduce two new graphical concepts---_imaginary subsets_ and _isolated edges_---that may be useful in their own right. As a matter of independent interest, the proofs also involve a novel characterization of the limits of edge orientations within the equivalence class of DAGs induced by _unknown_ interventions. These are the first results to characterize the conditions under which causal representations are identifiable without making any parametric assumptions in a general setting with unknown interventions and without faithfulness.

Contextual decision-making problems have witnessed extensive applications in various fields such as online content recommendation, personalized healthcare, and autonomous vehicles, where a core practical challenge is to select a suitable surrogate model for capturing unknown complicated reward functions. It is often the case that both high approximation accuracy and explicit uncertainty quantification are desired. In this work, we propose a neural network-accompanied Gaussian process (NN-AGP) model, which leverages neural networks to approximate the unknown and potentially complicated reward function regarding the contextual variable, and maintains a Gaussian process surrogate model with respect to the decision variable. Our model is shown to outperform existing approaches by offering better approximation accuracy thanks to the use of neural networks and possessing explicit uncertainty quantification from the Gaussian process. We also analyze the maximum information gain of the NN-AGP model and prove the regret bounds for the corresponding algorithms. Moreover, we conduct the experiments on both synthetic and practical problems, illustrating the effectiveness of our approach.

We propose a Bayesian encoder for metric learning. Rather than relying on neural amortization as done in prior works, we learn a distribution over the network weights with the Laplace Approximation. We first prove that the contrastive loss is a negative log-likelihood on the spherical space. We propose three methods that ensure a positive definite covariance matrix. Lastly, we present a novel decomposition of the Generalized Gauss-Newton approximation. Empirically, we show that our Laplacian Metric Learner (LAM) yields well-calibrated uncertainties, reliably detects out-of-distribution examples, and has state-of-the-art predictive performance.

Common statistical measures of uncertainty such as $p$-values and confidence intervals quantify the uncertainty due to sampling, that is, the uncertainty due to not observing the full population. However, sampling is not the only source of uncertainty. In practice, distributions change between locations and across time. This makes it difficult to gather knowledge that transfers across data sets. We propose a measure of instability that quantifies the distributional instability of a statistical parameter with respect to Kullback-Leibler divergence, that is, the sensitivity of the parameter under general distributional perturbations within a Kullback-Leibler divergence ball. In addition, we quantify the instability of parameters with respect to directional or variable-specific shifts. Measuring instability with respect to directional shifts can be used to detect under which kind of distribution shifts a statistical conclusion might be reversed. We discuss how such knowledge can inform data collection for transfer learning of statistical parameters under shifted distributions. We evaluate the performance of the proposed measure on real data and show that it can elucidate the distributional instability of a parameter with respect to certain shifts and can be used to improve estimation accuracy under shifted distributions.

High-energy collisions at the Large Hadron Collider (LHC) provide valuable insights into open questions in particle physics. However, detector effects must be corrected before measurements can be compared to certain theoretical predictions or measurements from other detectors. Methods to solve this inverse problem of mapping detector observations to theoretical quantities of the underlying collision are essential parts of many physics analyses at the LHC. We investigate and compare various generative deep learning methods to approximate this inverse mapping. We introduce a novel unified architecture, termed latent variational diffusion models, which combines the latent learning of cutting-edge generative art approaches with an end-to-end variational framework. We demonstrate the effectiveness of this approach for reconstructing global distributions of theoretical kinematic quantities, as well as for ensuring the adherence of the learned posterior distributions to known physics constraints. Our unified approach achieves a distribution-free distance to the truth of over 20 times smaller than non-latent state-of-the-art baseline and 3 times smaller than traditional latent diffusion models.

In unsupervised causal representation learning for sequential data with time-delayed latent causal influences, strong identifiability results for the disentanglement of causally-related latent variables have been established in stationary settings by leveraging temporal structure. However, in nonstationary setting, existing work only partially addressed the problem by either utilizing observed auxiliary variables (e.g., class labels and/or domain indexes) as side information or assuming simplified latent causal dynamics. Both constrain the method to a limited range of scenarios. In this study, we further explored the Markov Assumption under time-delayed causally related process in nonstationary setting and showed that under mild conditions, the independent latent components can be recovered from their nonlinear mixture up to a permutation and a component-wise transformation, without the observation of auxiliary variables. We then introduce NCTRL, a principled estimation framework, to reconstruct time-delayed latent causal variables and identify their relations from measured sequential data only. Empirical evaluations demonstrated the reliable identification of time-delayed latent causal influences, with our methodology substantially outperforming existing baselines that fail to exploit the nonstationarity adequately and then, consequently, cannot distinguish distribution shifts.

In this paper, we investigate the impact of numerical instability on the reliability of sampling, density evaluation, and evidence lower bound (ELBO) estimation in variational flows. We first empirically demonstrate that common flows can exhibit a catastrophic accumulation of error: the numerical flow map deviates significantly from the exact map---which affects sampling---and the numerical inverse flow map does not accurately recover the initial input---which affects density and ELBO computations. Surprisingly though, we find that results produced by flows are often accurate enough for applications despite the presence of serious numerical instability. In this work, we treat variational flows as chaotic dynamical systems, and leverage shadowing theory to elucidate this behavior via theoretical guarantees on the error of sampling, density evaluation, and ELBO estimation. Finally, we develop and empirically test a diagnostic procedure that can be used to validate results produced by numerically unstable flows in practice.

One of the goals of causal inference is to generalize from past experiments and observational data to novel conditions. While it is in principle possible to eventually learn a mapping from a novel experimental condition to an outcome of interest, provided a sufficient variety of experiments is available in the training data, coping with a large combinatorial space of possible interventions is hard. Under a typical sparse experimental design, this mapping is ill-posed without relying on heavy regularization or prior distributions. Such assumptions may or may not be reliable, and can be hard to defend or test. In this paper, we take a close look at how to warrant a leap from past experiments to novel conditions based on minimal assumptions about the factorization of the distribution of the manipulated system, communicated in the well-understood language of factor graph models. A postulated interventional factor model (IFM) may not always be informative, but it conveniently abstracts away a need for explicitly modeling unmeasured confounding and feedback mechanisms, leading to directly testable claims. Given an IFM and datasets from a collection of experimental regimes, we derive conditions for identifiability of the expected outcomes of new regimes never observed in these training data. We implement our framework using several efficient algorithms, and apply them on a range of semi-synthetic experiments.

Modern successes of diffusion models in learning complex, high-dimensional data distributions are attributed, in part, to their capability to construct diffusion processes with analytic transition kernels and score functions. The tractability results in a simulation-free framework with stable regression losses, from which reversed, generative processes can be learned at scale. However, when data is confined to a constrained set as opposed to a standard Euclidean space, these desirable characteristics appear to be lost based on prior attempts. In this work, we propose Mirror Diffusion Models (MDM), a new class of diffusion models that generate data on convex constrained sets without losing any tractability. This is achieved by learning diffusion processes in a dual space constructed from a mirror map, which, crucially, is a standard Euclidean space. We derive efficient computation of mirror maps for popular constrained sets, such as simplices and $\ell_2$-balls, showing significantly improved performance of MDM over existing methods. For safety and privacy purposes, we also explore constrained sets as a new mechanism to embed invisible but quantitative information (i.e., watermarks) in generated data, for which MDM serves as a compelling approach. Our work brings new algorithmic opportunities for learning tractable diffusion on complex domains.

Learning causal structures from interventional data is a fundamental problem with broad applications across various fields. While many previous works have focused on recovering the entire causal graph, in practice, there are scenarios where learning only part of the causal graph suffices. This is called \emph{targeted} causal discovery. In our work, we focus on two such well-motivated problems: subset search and causal matching. We aim to minimize the number of interventions in both cases. Towards this, we introduce the \emph{Meek separator}, which is a subset of vertices that, when intervened, decomposes the remaining unoriented edges into smaller connected components. We then present an efficient algorithm to find Meek separators that are of small sizes. Such a procedure is helpful in designing various divide-and-conquer-based approaches. In particular, we propose two randomized algorithms that achieve logarithmic approximation for subset search and causal matching, respectively. Our results provide the first known average-case provable guarantees for both problems. We believe that this opens up possibilities to design near-optimal methods for many other targeted causal structure learning problems arising from various applications.

Drawbacks of ignoring the causal mechanisms when performing imitation learning have recently been acknowledged. Several approaches both to assess the feasibility of imitation and to circumvent causal confounding and causal misspecifications have been proposed in the literature. However, the potential benefits of the incorporation of additional information about the underlying causal structure are left unexplored. An example of such overlooked information is context-specific independence (CSI), i.e., independence that holds only in certain contexts. We consider the problem of causal imitation learning when CSI relations are known. We prove that the decision problem pertaining to the feasibility of imitation in this setting is NP-hard. Further, we provide a necessary graphical criterion for imitation learning under CSI and show that under a structural assumption, this criterion is also sufficient. Finally, we propose a sound algorithmic approach for causal imitation learning which takes both CSI relations and data into account.

Causal disentanglement aims to uncover a representation of data using latent variables that are interrelated through a causal model. Such a representation is identifiable if the latent model that explains the data is unique. In this paper, we focus on the scenario where unpaired observational and interventional data are available, with each intervention changing the mechanism of a latent variable. When the causal variables are fully observed, statistically consistent algorithms have been developed to identify the causal model under faithfulness assumptions. We here show that identifiability can still be achieved with unobserved causal variables, given a generalized notion of faithfulness. Our results guarantee that we can recover the latent causal model up to an equivalence class and predict the effect of unseen combinations of interventions, in the limit of infinite data. We implement our causal disentanglement framework by developing an autoencoding variational Bayes algorithm and apply it to the problem of predicting combinatorial perturbation effects in genomics.

Irregularly sampled time series are increasingly prevalent, particularly in medical domains. While various specialized methods have been developed to handle these irregularities, effectively modeling their complex dynamics and pronounced sparsity remains a challenge. This paper introduces a novel perspective by converting irregularly sampled time series into line graph images, then utilizing powerful pre-trained vision transformers for time series classification in the same way as image classification. This method not only largely simplifies specialized algorithm designs but also presents the potential to serve as a universal framework for time series modeling. Remarkably, despite its simplicity, our approach outperforms state-of-the-art specialized algorithms on several popular healthcare and human activity datasets. Especially in the rigorous leave-sensors-out setting where a portion of variables is omitted during testing, our method exhibits strong robustness against varying degrees of missing observations, achieving an impressive improvement of 42.8% in absolute F1 score points over leading specialized baselines even with half the variables masked. Code and data are available at https://github.com/Leezekun/ViTST.

Researchers in explainable artificial intelligence have developed numerous methods for helping users understand the predictions of complex supervised learning models. By contrast, explaining the $\textit{uncertainty}$ of model outputs has received relatively little attention. We adapt the popular Shapley value framework to explain various types of predictive uncertainty, quantifying each feature's contribution to the conditional entropy of individual model outputs. We consider games with modified characteristic functions and find deep connections between the resulting Shapley values and fundamental quantities from information theory and conditional independence testing. We outline inference procedures for finite sample error rate control with provable guarantees, and implement efficient algorithms that perform well in a range of experiments on real and simulated data. Our method has applications to covariate shift detection, active learning, feature selection, and active feature-value acquisition.

Energy-based models are a simple yet powerful class of probabilistic models, but their widespread adoption has been limited by the computational burden of training them. We propose a novel loss function called Energy Discrepancy (ED) which does not rely on the computation of scores or expensive Markov chain Monte Carlo. We show that energy discrepancy approaches the explicit score matching and negative log-likelihood loss under different limits, effectively interpolating between both. Consequently, minimum energy discrepancy estimation overcomes the problem of nearsightedness encountered in score-based estimation methods, while also enjoying theoretical guarantees. Through numerical experiments, we demonstrate that ED learns low-dimensional data distributions faster and more accurately than explicit score matching or contrastive divergence. For high-dimensional image data, we describe how the manifold hypothesis puts limitations on our approach and demonstrate the effectiveness of energy discrepancy by training the energy-based model as a prior of a variational decoder model.

We introduce Markov Neural Processes (MNPs), a new class of Stochastic Processes (SPs) which are constructed by stacking sequences of neural parameterised Markov transition operators in function space. We prove that these Markov transition operators can preserve the exchangeability and consistency of SPs. Therefore, the proposed iterative construction adds substantial flexibility and expressivity to the original framework of Neural Processes (NPs) without compromising consistency or adding restrictions. Our experiments demonstrate clear advantages of MNPs over baseline models on a variety of tasks.

Gaussian processes (GPs) can provide a principled approach to uncertainty quantification with easy-to-interpret kernel hyperparameters, such as the lengthscale, which controls the correlation distance of function values.However, selecting an appropriate kernel can be challenging. Deep GPs avoid manual kernel engineering by successively parameterizing kernels with GP layers, allowing them to learn low-dimensional embeddings of the inputs that explain the output data. Following the architecture of deep neural networks, the most common deep GPs warp the input space layer-by-layer but lose all the interpretability of shallow GPs. An alternative construction is to successively parameterize the lengthscale of a kernel, improving the interpretability but ultimately giving away the notion of learning lower-dimensional embeddings. Unfortunately, both methods are susceptible to particular pathologies which may hinder fitting and limit their interpretability. This work proposes a novel synthesis of both previous approaches: {Thin and Deep GP} (TDGP). Each TDGP layer defines locally linear transformations of the original input data maintaining the concept of latent embeddings while also retaining the interpretation of lengthscales of a kernel. Moreover, unlike the prior solutions, TDGP induces non-pathological manifolds that admit learning lower-dimensional representations. We show with theoretical and experimental results that i) TDGP is, unlike previous models, tailored to specifically discover lower-dimensional manifolds in the input data, ii) TDGP behaves well when increasing the number of layers, and iii) TDGP performs well in standard benchmark datasets.

Diffusion models are a class of generative models that serve to establish a stochastic transport map between an empirically observed, yet unknown, target distribution and a known prior. Despite their remarkable success in real-world applications, a theoretical understanding of their generalization capabilities remains underdeveloped. This work embarks on a comprehensive theoretical exploration of the generalization attributes of diffusion models. We establish the theoretical estimates of the generalization gap that evolves in tandem with the training dynamics of score-based diffusion models, suggesting a polynomially small generalization error ($O(n^{-2/5}+m^{-4/5})$) on both the sample size $n$ and the model capacity $m$, evading the curse of dimensionality (i.e., independent of the data dimension) when *early-stopped*. Furthermore, we extend our quantitative analysis to a *data-dependent* scenario, wherein target distributions are portrayed as a succession of densities with progressively increasing distances between modes. This precisely elucidates the *adverse* effect of "*modes shift*'' in ground truths on the model generalization. Furthermore, these estimates are not solely theoretical constructs but have also been confirmed through numerical simulations. Our findings contribute to the rigorous understanding of diffusion models' generalization properties and provide insights that may guide practical applications.

The average treatment effect, which is the difference in expectation of the counterfactuals, is probably the most popular target effect in causal inference with binary treatments. However, treatments may have effects beyond the mean, for instance decreasing or increasing the variance. We propose a new kernel-based test for distributional effects of the treatment. It is, to the best of our knowledge, the first kernel-based, doubly-robust test with provably valid type-I error. Furthermore, our proposed algorithm is computationally efficient, avoiding the use of permutations.

The Finite Element Method, an important technique in engineering, is aided by Adaptive Mesh Refinement (AMR), which dynamically refines mesh regions to allow for a favorable trade-off between computational speed and simulation accuracy. Classical methods for AMR depend on task-specific heuristics or expensive error estimators, hindering their use for complex simulations. Recent learned AMR methods tackle these problems, but so far scale only to simple toy examples. We formulate AMR as a novel Adaptive Swarm Markov Decision Process in which a mesh is modeled as a system of simple collaborating agents that may split into multiple new agents. This framework allows for a spatial reward formulation that simplifies the credit assignment problem, which we combine with Message Passing Networks to propagate information between neighboring mesh elements. We experimentally validate the effectiveness of our approach, Adaptive Swarm Mesh Refinement (ASMR), showing that it learns reliable, scalable, and efficient refinement strategies on a set of challenging problems. Our approach significantly speeds up computation, achieving up to 30-fold improvement compared to uniform refinements in complex simulations. Additionally, we outperform learned baselines and achieve a refinement quality that is on par with a traditional error-based AMR strategy without expensive oracle information about the error signal.

We study data-driven decision-making problems in the Bayesian framework, where the expectation in the Bayes risk is replaced by a risk-sensitive entropic risk measure with respect to the posterior distribution. We focus on problems where calculating the posterior distribution is intractable, a typical situation in modern applications with large datasets and complex data generating models. We leverage a dual representation of the entropic risk measure to introduce a novel risk-sensitive variational Bayesian (RSVB) framework for jointly computing a risk-sensitive posterior approximation and the corresponding decision rule. Our general framework includes \textit{loss-calibrated} VB (Lacoste-Julien et al. [2011] ) as a special case. We also study the impact of these computational approximations on the predictive performance of the inferred decision rules. We compute the convergence rates of the RSVB approximate posterior and the corresponding optimal value. We illustrate our theoretical findings in parametric and nonparametric settings with the help of three examples.

Recently, operator learning, or learning mappings between infinite-dimensional function spaces, has garnered significant attention, notably in relation to learning partial differential equations from data. Conceptually clear when outlined on paper, neural operators necessitate discretization in the transition to computer implementations. This step can compromise their integrity, often causing them to deviate from the underlying operators. This research offers a fresh take on neural operators with a framework Representation equivalent Neural Operators (ReNO) designed to address these issues. At its core is the concept of operator aliasing, which measures inconsistency between neural operators and their discrete representations. We explore this for widely-used operator learning techniques. Our findings detail how aliasing introduces errors when handling different discretizations and grids and loss of crucial continuous structures. More generally, this framework not only sheds light on existing challenges but, given its constructive and broad nature, also potentially offers tools for developing new neural operators.

Bayesian neural networks (BNNs) provide a formalism to quantify and calibrate uncertainty in deep learning. Current inference approaches for BNNs often resort to few-sample estimation for scalability, which can harm predictive performance, while its alternatives tend to be computationally prohibitively expensive. We tackle this challenge by revealing a previously unseen connection between inference on BNNs and volume computation problems. With this observation, we introduce a novel collapsed inference scheme that performs Bayesian model averaging using collapsed samples. It improves over a Monte-Carlo sample by limiting sampling to a subset of the network weights while pairing it with some closed-form conditional distribution over the rest. A collapsed sample represents uncountably many models drawn from the approximate posterior and thus yields higher sample efficiency. Further, we show that the marginalization of a collapsed sample can be solved analytically and efficiently despite the non-linearity of neural networks by leveraging existing volume computation solvers. Our proposed use of collapsed samples achieves a balance between scalability and accuracy. On various regression and classification tasks, our collapsed Bayesian deep learning approach demonstrates significant improvements over existing methods and sets a new state of the art in terms of uncertainty estimation as well as predictive performance.

We study reinforcement learning (RL) in the setting of continuous time and space, for an infinite horizon with a discounted objective and the underlying dynamics driven by a stochastic differential equation. Built upon recent advances in the continuous approach to RL, we develop a notion of occupation time (specifically for a discounted objective), and show how it can be effectively used to derive performance difference and local approximation formulas. We further extend these results to illustrate their applications in the PG (policy gradient) and TRPO/PPO (trust region policy optimization/ proximal policy optimization) methods, which have been familiar and powerful tools in the discrete RL setting but under-developed in continuous RL. Through numerical experiments, we demonstrate the effectiveness and advantages of our approach.

One of the fundamental challenges found throughout the data sciences is to explain why things happen in specific ways, or through which mechanisms a certain variable $X$ exerts influences over another variable $Y$. In statistics and machine learning, significant efforts have been put into developing machinery to estimate correlations across variables efficiently. In causal inference, a large body of literature is concerned with the decomposition of causal effects under the rubric of mediation analysis. However, many variations are spurious in nature, including different phenomena throughout the applied sciences. Despite the statistical power to estimate correlations and the identification power to decompose causal effects, there is still little understanding of the properties of spurious associations and how they can be decomposed in terms of the underlying causal mechanisms. In this manuscript, we develop formal tools for decomposing spurious variations in both Markovian and Semi-Markovian models. We prove the first results that allow a non-parametric decomposition of spurious effects and provide sufficient conditions for the identification of such decompositions. The described approach has several applications, ranging from explainable and fair AI to questions in epidemiology and medicine, and we empirically demonstrate its use on a real-world dataset.

Stein Variational Gradient Descent (SVGD) is a nonparametric particle-based deterministic sampling algorithm. Despite its wide usage, understanding the theoretical properties of SVGD has remained a challenging problem. For sampling from a Gaussian target, the SVGD dynamics with a bilinear kernel will remain Gaussian as long as the initializer is Gaussian. Inspired by this fact, we undertake a detailed theoretical study of the Gaussian-SVGD, i.e., SVGD projected to the family of Gaussian distributions via the bilinear kernel, or equivalently Gaussian variational inference (GVI) with SVGD. We present a complete picture by considering both the mean-field PDE and discrete particle systems. When the target is strongly log-concave, the mean-field Gaussian-SVGD dynamics is proven to converge linearly to the Gaussian distribution closest to the target in KL divergence. In the finite-particle setting, there is both uniform in time convergence to the mean-field limit and linear convergence in time to the equilibrium if the target is Gaussian. In the general case, we propose a density-based and a particle-based implementation of the Gaussian-SVGD, and show that several recent algorithms for GVI, proposed from different perspectives, emerge as special cases of our unified framework. Interestingly, one of the new particle-based instance from this framework empirically outperforms existing approaches. Our results make concrete contributions towards obtaining a deeper understanding of both SVGD and GVI.

The control of continuous-time environments while actively deciding when to take costly observations in time is a crucial yet unexplored problem, particularly relevant to real-world scenarios such as medicine, low-power systems, and resource management. Existing approaches either rely on continuous-time control methods that take regular, expensive observations in time or discrete-time control with costly observation methods, which are inapplicable to continuous-time settings due to the compounding discretization errors introduced by time discretization. In this work, we are the first to formalize the continuous-time control problem with costly observations. Our key theoretical contribution shows that observing at regular time intervals is not optimal in certain environments, while irregular observation policies yield higher expected utility. This perspective paves the way for the development of novel methods that can take irregular observations in continuous-time control with costly observations. We empirically validate our theoretical findings in various continuous-time environments, including a cancer simulation, by constructing a simple initial method to solve this new problem, with a heuristic threshold on the variance of reward rollouts in an offline continuous-time model-based model predictive control (MPC) planner. Although determining the optimal method remains an open problem, our work offers valuable insights and understanding of this unique problem, laying the foundation for future research in this area.

We develop an advanced approach for extending Gaussian Differential Privacy (GDP) to general Riemannian manifolds. The concept of GDP stands out as a prominent privacy definition that strongly warrants extension to manifold settings, due to its central limit properties. By harnessing the power of the renowned Bishop-Gromov theorem in geometric analysis, we propose a Riemannian Gaussian distribution that integrates the Riemannian distance, allowing us to achieve GDP in Riemannian manifolds with bounded Ricci curvature. To the best of our knowledge, this work marks the first instance of extending the GDP framework to accommodate general Riemannian manifolds, encompassing curved spaces, and circumventing the reliance on tangent space summaries. We provide a simple algorithm to evaluate the privacy budget $\mu$ on any one-dimensional manifold and introduce a versatile Markov Chain Monte Carlo (MCMC)-based algorithm to calculate $\mu$ on any Riemannian manifold with constant curvature. Through simulations on one of the most prevalent manifolds in statistics, the unit sphere $S^d$, we demonstrate the superior utility of our Riemannian Gaussian mechanism in comparison to the previously proposed Riemannian Laplace mechanism for implementing GDP.

Probabilistic inference in high-dimensional state-space models is computationally challenging. For many spatiotemporal systems, however, prior knowledge about the dependency structure of state variables is available. We leverage this structure to develop a computationally efficient approach to state estimation and learning in graph-structured state-space models with (partially) unknown dynamics and limited historical data. Building on recent methods that combine ideas from deep learning with principled inference in Gaussian Markov random fields (GMRF), we reformulate graph-structured state-space models as Deep GMRFs defined by simple spatial and temporal graph layers. This results in a flexible spatiotemporal prior that can be learned efficiently from a single time sequence via variational inference. Under linear Gaussian assumptions, we retain a closed-form posterior, which can be sampled efficiently using the conjugate gradient method, scaling favourably compared to classical Kalman filter based approaches.

Motion planning is still an open problem for many disciplines, e.g., robotics, autonomous driving, due to their need for high computational resources that hinder real-time, efficient decision-making. A class of methods striving to provide smooth solutions is gradient-based trajectory optimization. However, those methods usually suffer from bad local minima, while for many settings, they may be inapplicable due to the absence of easy-to-access gradients of the optimization objectives. In response to these issues, we introduce Motion Planning via Optimal Transport (MPOT)---a \textit{gradient-free} method that optimizes a batch of smooth trajectories over highly nonlinear costs, even for high-dimensional tasks, while imposing smoothness through a Gaussian Process dynamics prior via the planning-as-inference perspective. To facilitate batch trajectory optimization, we introduce an original zero-order and highly-parallelizable update rule----the Sinkhorn Step, which uses the regular polytope family for its search directions. Each regular polytope, centered on trajectory waypoints, serves as a local cost-probing neighborhood, acting as a \textit{trust region} where the Sinkhorn Step ``transports'' local waypoints toward low-cost regions. We theoretically show that Sinkhorn Step guides the optimizing parameters toward local minima regions of non-convex objective functions. We then show the efficiency of MPOT in a range of problems from low-dimensional point-mass navigation to high-dimensional whole-body robot motion planning, evincing its superiority compared to popular motion planners, paving the way for new applications of optimal transport in motion planning.

This paper addresses the problem of localizing and inferring multiple change points, in non-parametric multivariate time series settings. Specifically, we consider a multivariate time series with potentially short-range dependence, whose underlying distributions have Hölder smooth densities and can change over time in a piecewise-constant manner. The change points, which correspond to the times when the distribution changes, are unknown. We present the limiting distributions of the change point estimators under the scenarios where the minimal jump size vanishes or remains constant. Such results have not been revealed in the literature in non-parametric change point settings. As byproducts, we develop a sharp estimator that can accurately localize the change points in multivariate non-parametric time series, and a consistent block-type long-run variance estimator. Numerical studies are provided to complement our theoretical findings.

Independent component analysis (ICA) is a fundamental statistical tool used to reveal hidden generative processes from observed data. However, traditional ICA approaches struggle with the rotational invariance inherent in Gaussian distributions, often necessitating the assumption of non-Gaussianity in the underlying sources. This may limit their applicability in broader contexts. To accommodate Gaussian sources, we develop an identifiability theory that relies on second-order statistics without imposing further preconditions on the distribution of sources, by introducing novel assumptions on the connective structure from sources to observed variables. Different from recent work that focuses on potentially restrictive connective structures, our proposed assumption of structural variability is both considerably less restrictive and provably necessary. Furthermore, we propose two estimation methods based on second-order statistics and sparsity constraint. Experimental results are provided to validate our identifiability theory and estimation methods.

The relevance of optimal transport methods to machine learning has long been hindered by two salient limitations. First, the $O(n^3)$ computational cost of standard sample-based solvers (when used on batches of $n$ samples) is prohibitive. Second, the mass conservation constraint makes OT solvers too rigid in practice: because they must match \textit{all} points from both measures, their output can be heavily influenced by outliers. A flurry of recent works in OT has addressed these computational and modelling limitations, but has resulted in two separate strains of methods: While the computational outlook was much improved by entropic regularization, more recent $O(n)$ linear-time \textit{low-rank} solvers hold the promise to scale up OT further. On the other hand, modelling rigidities have been eased owing to unbalanced variants of OT, that rely on penalization terms to promote, rather than impose, mass conservation. The goal of this paper is to merge these two strains, to achieve the promise of \textit{both} versatile/scalable unbalanced/low-rank OT solvers. We propose custom algorithms to implement these extensions for the linear OT problem and its Fused-Gromov-Wasserstein generalization, and demonstrate their practical relevance to challenging spatial transcriptomics matching problems.

Categorical random variables can faithfully represent the discrete and uncertain aspects of data as part of a discrete latent variable model. Learning in such models necessitates taking gradients with respect to the parameters of the categorical probability distributions, which is often intractable due to their combinatorial nature. A popular technique to estimate these otherwise intractable gradients is the Log-Derivative trick. This trick forms the basis of the well-known REINFORCE gradient estimator and its many extensions. While the Log-Derivative trick allows us to differentiate through samples drawn from categorical distributions, it does not take into account the discrete nature of the distribution itself. Our first contribution addresses this shortcoming by introducing the CatLog-Derivative trick -- a variation of the Log-Derivative trick tailored towards categorical distributions. Secondly, we use the CatLog-Derivative trick to introduce IndeCateR, a novel and unbiased gradient estimator for the important case of products of independent categorical distributions with provably lower variance than REINFORCE. Thirdly, we empirically show that IndeCateR can be efficiently implemented and that its gradient estimates have significantly lower bias and variance for the same number of samples compared to the state of the art.

We propose a novel approach to learning the generative neural fields represented by linear combinations of implicit basis networks. Our algorithm learns basis networks in the form of implicit neural representations and their coefficients in a latent space by either conducting meta-learning or adopting auto-decoding paradigms. The proposed method easily enlarges the capacity of generative neural fields by increasing the number of basis networks while maintaining the size of a network for inference to be small through their weighted model averaging. Consequently, sampling instances using the model is efficient in terms of latency and memory footprint. Moreover, we customize denoising diffusion probabilistic model for a target task to sample latent mixture coefficients, which allows our final model to generate unseen data effectively. Experiments show that our approach achieves competitive generation performance on diverse benchmarks for images, voxel data, and NeRF scenes without sophisticated designs for specific modalities and domains.

Monte-Carlo Tree Search (MCTS) methods, such as Upper Confidence Bound applied to Trees (UCT), are instrumental to automated planning techniques. However, UCT can be slow to explore an optimal action when it initially appears inferior to other actions. Maximum ENtropy Tree-Search (MENTS) incorporates the maximum entropy principle into an MCTS approach, utilising Boltzmann policies to sample actions, naturally encouraging more exploration. In this paper, we highlight a major limitation of MENTS: optimal actions for the maximum entropy objective do not necessarily correspond to optimal actions for the original objective. We introduce two algorithms, Boltzmann Tree Search (BTS) and Decaying ENtropy Tree-Search (DENTS), that address these limitations and preserve the benefits of Boltzmann policies, such as allowing actions to be sampled faster by using the Alias method. Our empirical analysis shows that our algorithms show consistent high performance across several benchmark domains, including the game of Go.

Inverse problems describe the task of recovering an underlying signal of interest given observables. Typically, the observables are related via some non-linear forward model applied to the underlying unknown signal. Inverting the non-linear forward model can be computationally expensive, as it often involves computing and inverting a linearization at a series of estimates. Rather than inverting the physics-based model, we instead train a surrogate forward model (emulator) and leverage modern auto-grad libraries to solve for the input within a classical optimization framework. Current methods to train emulators are done in a black box supervised machine learning fashion and fail to take advantage of any existing knowledge of the forward model. In this article, we propose a simple learned weighted average model that embeds linearizations of the forward model around various reference points into the model itself, explicitly incorporating known physics. Grounding the learned model with physics based linearizations improves the forward modeling accuracy and provides richer physics based gradient information during the inversion process leading to more accurate signal recovery. We demonstrate the efficacy on an ocean acoustic tomography (OAT) example that aims to recover ocean sound speed profile (SSP) variations from acoustic observations (e.g. eigenray arrival times) within simulation of ocean dynamics in the Gulf of Mexico.

We consider the problem of inferring latent stochastic differential equations (SDEs) with a time and memory cost that scales independently with the amount of data, the total length of the time series, and the stiffness of the approximate differential equations. This is in stark contrast to typical methods for inferring latent differential equations which, despite their constant memory cost, have a time complexity that is heavily dependent on the stiffness of the approximate differential equation. We achieve this computational advancement by removing the need to solve differential equations when approximating gradients using a novel amortization strategy coupled with a recently derived reparametrization of expectations under linear SDEs. We show that, in practice, this allows us to achieve similar performance to methods based on adjoint sensitivities with more than an order of magnitude fewer evaluations of the model in training.

In many scientific applications, we observe a system in different conditions in which its components may change, rather than in isolation. In our work, we are interested in explaining the generating process of such a multi-context system using a finite mixture of causal mechanisms. Recent work shows that this causal model is identifiable from data, but is limited to settings where the sparse mechanism shift hypothesis holds and only a subset of the causal conditionals change. As this assumption is not easily verifiable in practice, we study the more general principle that mechanism shifts are independent, which we formalize using the algorithmic notion of independence. We introduce an approach for causal discovery beyond partially directed graphs using Gaussian Process models, and give conditions under which we provably identify the correct causal model. In our experiments, we show that our method performs well in a range of synthetic settings, on realistic gene expression simulations, as well as on real-world cell signaling data.

Energy-Based Models (EBMs) offer a versatile framework for modelling complex data distributions. However, training and sampling from EBMs continue to pose significant challenges. The widely-used Denoising Score Matching (DSM) method for scalable EBM training suffers from inconsistency issues, causing the energy model to learn a noisy data distribution. In this work, we propose an efficient sampling framework: (pseudo)-Gibbs sampling with moment matching, which enables effective sampling from the underlying clean model when given a noisy model that has been well-trained via DSM. We explore the benefits of our approach compared to related methods and demonstrate how to scale the method to high-dimensional datasets.

Neural networks are emerging as a tool for scalable data-driven simulation of high-dimensional dynamical systems, especially in settings where numerical methods are infeasible or computationally expensive. Notably, it has been shown that incorporating domain symmetries in deterministic neural simulators can substantially improve their accuracy, sample efficiency, and parameter efficiency. However, to incorporate symmetries in probabilistic neural simulators that can simulate stochastic phenomena, we need a model that produces equivariant distributions over trajectories, rather than equivariant function approximations. In this paper, we propose Equivariant Probabilistic Neural Simulation (EPNS), a framework for autoregressive probabilistic modeling of equivariant distributions over system evolutions. We use EPNS to design models for a stochastic n-body system and stochastic cellular dynamics. Our results show that EPNS considerably outperforms existing neural network-based methods for probabilistic simulation. More specifically, we demonstrate that incorporating equivariance in EPNS improves simulation quality, data efficiency, rollout stability, and uncertainty quantification. We conclude that EPNS is a promising method for efficient and effective data-driven probabilistic simulation in a diverse range of domains.

Probabilistic solvers provide a flexible and efficient framework for simulation, uncertainty quantification, and inference in dynamical systems. However, like standard solvers, they suffer performance penalties for certain stiff systems, where small steps are required not for reasons of numerical accuracy but for the sake of stability. This issue is greatly alleviated in semi-linear problems by the probabilistic exponential integrators developed in this paper. By including the fast, linear dynamics in the prior, we arrive at a class of probabilistic integrators with favorable properties. Namely, they are proven to be L-stable, and in a certain case reduce to a classic exponential integrator---with the added benefit of providing a probabilistic account of the numerical error. The method is also generalized to arbitrary non-linear systems by imposing piece-wise semi-linearity on the prior via Jacobians of the vector field at the previous estimates, resulting in probabilistic exponential Rosenbrock methods. We evaluate the proposed methods on multiple stiff differential equations and demonstrate their improved stability and efficiency over established probabilistic solvers. The present contribution thus expands the range of problems that can be effectively tackled within probabilistic numerics.

While complex simulations of physical systems have been widely used in engineering and scientific computing, lowering their often prohibitive computational requirements has only recently been tackled by deep learning approaches. In this paper, we present GraphSplineNets, a novel deep-learning method to speed up the forecasting of physical systems by reducing the grid size and number of iteration steps of deep surrogate models. Our method uses two differentiable orthogonal spline collocation methods to efficiently predict response at any location in time and space. Additionally, we introduce an adaptive collocation strategy in space to prioritize sampling from the most important regions. GraphSplineNets improve the accuracy-speedup tradeoff in forecasting various dynamical systems with increasing complexity, including the heat equation, damped wave propagation, Navier-Stokes equations, and real-world ocean currents in both regular and irregular domains.

Partitioning a set of elements into an unknown number of mutually exclusive subsets is essential in many machine learning problems. However, assigning elements, such as samples in a dataset or neurons in a network layer, to an unknown and discrete number of subsets is inherently non-differentiable, prohibiting end-to-end gradient-based optimization of parameters. We overcome this limitation by proposing a novel two-step method for inferring partitions, which allows its usage in variational inference tasks. This new approach enables reparameterized gradients with respect to the parameters of the new random partition model. Our method works by inferring the number of elements per subset and, second, by filling these subsets in a learned order. We highlight the versatility of our general-purpose approach on three different challenging experiments: variational clustering, inference of shared and independent generative factors under weak supervision, and multitask learning.

The accurate predictions and principled uncertainty measures provided by GP regression incur $O(n^3)$ cost which is prohibitive for modern-day large-scale applications. This has motivated extensive work on computationally efficient approximations. We introduce a new perspective by exploring robustness properties and limiting behaviour of GP nearest-neighbour (GPnn) prediction. We demonstrate through theory and simulation that as the data-size $n$ increases, accuracy of estimated parameters and GP model assumptions become increasingly irrelevant to GPnn predictive accuracy. Consequently, it is sufficient to spend small amounts of work on parameter estimation in order to achieve high MSE accuracy, even in the presence of gross misspecification. In contrast, as $n \rightarrow \infty$, uncertainty calibration and NLL are shown to remain sensitive to just one parameter, the additive noise-variance; but we show that this source of inaccuracy can be corrected for, thereby achieving both well-calibrated uncertainty measures and accurate predictions at remarkably low computational cost. We exhibit a very simple GPnn regression algorithm with stand-out performance compared to other state-of-the-art GP approximations as measured on large UCI datasets. It operates at a small fraction of those other methods' training costs, for example on a basic laptop taking about 30 seconds to train on a dataset of size $n = 1.6 \times 10^6$.

The well-established practice of time series analysis involves estimating deterministic, non-stationary trend and seasonality components followed by learning the residual stochastic, stationary components. Recently, it has been shown that one can learn the deterministic non-stationary components accurately using multivariate Singular Spectrum Analysis (mSSA) in the absence of a correlated stationary component; meanwhile, in the absence of deterministic non-stationary components, the Autoregressive (AR) stationary component can also be learnt readily, e.g. via Ordinary Least Squares (OLS). However, a theoretical underpinning of multi-stage learning algorithms involving both deterministic and stationary components has been absent in the literature despite its pervasiveness. We resolve this open question by establishing desirable theoretical guarantees for a natural two-stage algorithm, where mSSA is first applied to estimate the non-stationary components despite the presence of a correlated stationary AR component, which is subsequently learned from the residual time series. We provide a finite-sample forecasting consistency bound for the proposed algorithm, SAMoSSA, which is data-driven and thus requires minimal parameter tuning. To establish theoretical guarantees, we overcome three hurdles: (i) we characterize the spectra of Page matrices of stable AR processes, thus extending the analysis of mSSA; (ii) we extend the analysis of AR process identification in the presence of arbitrary bounded perturbations; (iii) we characterize the out-of-sample or forecasting error, as opposed to solely considering model identification. Through representative empirical studies, we validate the superior performance of SAMoSSA compared to existing baselines. Notably, SAMoSSA's ability to account for AR noise structure yields improvements ranging from 5% to 37% across various benchmark datasets.

In many applications of machine learning, a large number of variables are considered. Motivated by machine learning of interacting particle systems, we consider the situation when the number of input variables goes to infinity. First, we continue the recent investigation of the mean field limit of kernels and their reproducing kernel Hilbert spaces, completing the existing theory. Next, we provide results relevant for approximation with such kernels in the mean field limit, including a representer theorem. Finally, we use these kernels in the context of statistical learning in the mean field limit, focusing on Support Vector Machines. In particular, we show mean field convergence of empirical and infinite-sample solutions as well as the convergence of the corresponding risks. On the one hand, our results establish rigorous mean field limits in the context of kernel methods, providing new theoretical tools and insights for large-scale problems. On the other hand, our setting corresponds to a new form of limit of learning problems, which seems to have not been investigated yet in the statistical learning theory literature.

Modeling continuous-time dynamics on irregular time series is critical to account for data evolution and correlations that occur continuously. Traditional methods including recurrent neural networks or Transformer models leverage inductive bias via powerful neural architectures to capture complex patterns. However, due to their discrete characteristic, they have limitations in generalizing to continuous-time data paradigms. Though neural ordinary differential equations (Neural ODEs) and their variants have shown promising results in dealing with irregular time series, they often fail to capture the intricate correlations within these sequences. It is challenging yet demanding to concurrently model the relationship between input data points and capture the dynamic changes of the continuous-time system. To tackle this problem, we propose ContiFormer that extends the relation modeling of vanilla Transformer to the continuous-time domain, which explicitly incorporates the modeling abilities of continuous dynamics of Neural ODEs with the attention mechanism of Transformers. We mathematically characterize the expressive power of ContiFormer and illustrate that, by curated designs of function hypothesis, many Transformer variants specialized in irregular time series modeling can be covered as a special case of ContiFormer. A wide range of experiments on both synthetic and real-world datasets have illustrated the superior modeling capacities and prediction performance of ContiFormer on irregular time series data. The project link is https://seqml.github.io/contiformer/.

In this paper, we critically examine the prevalent practice of using additive mixtures of Mat\'ern kernels in single-output Gaussian process (GP) models and explore the properties of multiplicative mixtures of Mat\'ern kernels for multi-output GP models. For the single-output case, we derive a series of theoretical results showing that the smoothness of a mixture of Mat\'ern kernels is determined by the least smooth component and that a GP with such a kernel is effectively equivalent to the least smooth kernel component. Furthermore, we demonstrate that none of the mixing weights or parameters within individual kernel components are identifiable. We then turn our attention to multi-output GP models and analyze the identifiability of the covariance matrix $A$ in the multiplicative kernel $K(x,y) = AK_0(x,y)$, where $K_0$ is a standard single output kernel such as Mat\'ern. We show that $A$ is identifiable up to a multiplicative constant, suggesting that multiplicative mixtures are well suited for multi-output tasks. Our findings are supported by extensive simulations and real applications for both single- and multi-output settings. This work provides insight into kernel selection and interpretation for GP models, emphasizing the importance of choosing appropriate kernel structures for different tasks.

Reinforcement learning algorithms typically consider discrete-time dynamics, even though the underlying systems are often continuous in time. In this paper, we introduce a model-based reinforcement learning algorithm that represents continuous-time dynamics using nonlinear ordinary differential equations (ODEs). We capture epistemic uncertainty using well-calibrated probabilistic models, and use the optimistic principle for exploration. Our regret bounds surface the importance of the measurement selection strategy (MSS), since in continuous time we not only must decide how to explore, but also when to observe the underlying system. Our analysis demonstrates that the regret is sublinear when modeling ODEs with Gaussian Processes (GP) for common choices of MSS, such as equidistant sampling. Additionally, we propose an adaptive, data-dependent, practical MSS that, when combined with GP dynamics, also achieves sublinear regret with significantly fewer samples. We showcase the benefits of continuous-time modeling over its discrete-time counterpart, as well as our proposed adaptive MSS over standard baselines, on several applications.

Neuro-symbolic AI bridges the gap between purely symbolic and neural approaches to learning. This often requires maximizing the likelihood of a symbolic constraint w.r.t the neural network's output distribution. Such output distributions are typically assumed to be fully-factorized. This limits the applicability of neuro-symbolic learning to the more expressive auto-regressive distributions, e.g., transformers. Under such distributions, computing the likelihood of even simple constraints is #P-hard. Instead of attempting to enforce the constraint on the entire likelihood distribution, we propose to do so on a random, local approximation thereof. More precisely, we approximate the likelihood of the constraint with the pseudolikelihood of the constraint centered around a model sample. Our approach is factorizable, allowing us to reuse solutions to sub-problems---a main tenet for the efficient computation of neuro-symbolic losses. It also provides a local, high fidelity approximation of the likelihood: it exhibits low entropy and KL-divergence around the model sample. We tested our approach on Sudoku and shortest-path prediction cast as auto-regressive generation, and observe that we greatly improve upon the base model's ability to predict logically-consistent outputs. We also tested our approach on the task of detoxifying large language models. We observe that using a simple constraint disallowing a list of toxic words, we are able to steer the model's outputs away from toxic generations, achieving SoTA compared to previous approaches.

In this paper, we introduce a novel MCMC sampler, PARNI-DAG, for a fully-Bayesian approach to the problem of structure learning under observational data. Under the assumption of causal sufficiency, the algorithm allows for approximate sampling directly from the posterior distribution on Directed Acyclic Graphs (DAGs). PARNI-DAG performs efficient sampling of DAGs via locally informed, adaptive random neighborhood proposal that results in better mixing properties. In addition, to ensure better scalability with the number of nodes, we couple PARNI-DAG with a pre-tuning procedure of the sampler's parameters that exploits a skeleton graph derived through some constraint-based or scoring-based algorithms. Thanks to these novel features, PARNI-DAG quickly converges to high-probability regions and is less likely to get stuck in local modes in the presence of high correlation between nodes in high-dimensional settings. After introducing the technical novelties in PARNI-DAG, we empirically demonstrate its mixing efficiency and accuracy in learning DAG structures on a variety of experiments.

MCMC algorithms offer empirically efficient tools for sampling from a target distribution $\pi(x) \propto \exp(-V(x))$. However, on the theory side, MCMC algorithms suffer from slow mixing rate when $\pi(x)$ is non-log-concave. Our work examines this gap and shows that when Poincar\'e-style inequality holds on a subset $\mathcal{X}$ of the state space, the conditional distribution of MCMC iterates over $\mathcal{X}$ mixes fast to the true conditional distribution. This fast mixing guarantee can hold in cases when global mixing is provably slow. We formalize the statement and quantify the conditional mixing rate. We further show that conditional mixing can have interesting implications for sampling from mixtures of Gaussians, parameter estimation for Gaussian mixture models, and Gibbs-sampling with well-connected local minima.

In this paper we compare and contrast the behavior of the posterior predictive distribution to the risk of the the maximum a posteriori estimator for the random features regression model in the overparameterized regime. We will focus on the variance of the posterior predictive distribution (Bayesian model average) and compare its asymptotics to that of the risk of the MAP estimator. In the regime where the model dimensions grow faster than any constant multiple of the number of samples, asymptotic agreement between these two quantities is governed by the phase transition in the signal-to-noise ratio. They also asymptotically agree with each other when the number of samples grow faster than any constant multiple of model dimensions. Numerical simulations illustrate finer distributional properties of the two quantities for finite dimensions. We conjecture they have Gaussian fluctuations and exhibit similar properties as found by previous authors in a Gaussian sequence model, this is of independent theoretical interest.

Kernel density estimation (KDE) is integral to a range of generative and discriminative tasks in machine learning. Drawing upon tools from the multidimensional calculus of variations, we derive an optimal weight function that reduces bias in standard kernel density estimates for density ratios, leading to improved estimates of prediction posteriors and information-theoretic measures. In the process, we shed light on some fundamental aspects of density estimation, particularly from the perspective of algorithms that employ KDEs as their main building blocks.

Gaussian Process Networks (GPNs) are a class of directed graphical models which employ Gaussian processes as priors for the conditional expectation of each variable given its parents in the network. The model allows the description of continuous joint distributions in a compact but flexible manner with minimal parametric assumptions on the dependencies between variables. Bayesian structure learning of GPNs requires computing the posterior over graphs of the network and is computationally infeasible even in low dimensions. This work implements Monte Carlo and Markov Chain Monte Carlo methods to sample from the posterior distribution of network structures. As such, the approach follows the Bayesian paradigm, comparing models via their marginal likelihood and computing the posterior probability of the GPN features. Simulation studies show that our method outperforms state-of-the-art algorithms in recovering the graphical structure of the network and provides an accurate approximation of its posterior distribution.

A new technique for unsupervised learning of time series data based on the notion of Granger causality is presented. The technique learns pairs of projections of a multivariate data set such that the resulting components -- "driving" and "driven" -- maximize the strength of the Granger causality between the latent time series (how strongly the past of the driving signal predicts the present of the driven signal). A coordinate descent algorithm that learns pairs of coefficient vectors in an alternating fashion is developed and shown to blindly identify the underlying sources (up to scale) on simulated vector autoregressive (VAR) data. The technique is tested on scalp electroencephalography (EEG) data from a motor imagery experiment where the resulting components lateralize with the side of the cued hand, and also on functional magnetic resonance imaging (fMRI) data, where the recovered components express previously reported resting-state networks.

Efficiently sampling from un-normalized target distributions is a fundamental problem in scientific computing and machine learning. Traditional approaches such as Markov Chain Monte Carlo (MCMC) guarantee asymptotically unbiased samples from such distributions but suffer from computational inefficiency, particularly when dealing with high-dimensional targets, as they require numerous iterations to generate a batch of samples. In this paper, we introduce an efficient and scalable neural implicit sampler that overcomes these limitations. The implicit sampler can generate large batches of samples with low computational costs by leveraging a neural transformation that directly maps easily sampled latent vectors to target samples without the need for iterative procedures. To train the neural implicit samplers, we introduce two novel methods: the KL training method and the Fisher training method. The former method minimizes the Kullback-Leibler divergence, while the latter minimizes the Fisher divergence between the sampler and the target distributions. By employing the two training methods, we effectively optimize the neural implicit samplers to learn and generate from the desired target distribution. To demonstrate the effectiveness, efficiency, and scalability of our proposed samplers, we evaluate them on three sampling benchmarks with different scales. These benchmarks include sampling from 2D targets, Bayesian inference, and sampling from high-dimensional energy-based models (EBMs). Notably, in the experiment involving high-dimensional EBMs, our sampler produces samples that are comparable to those generated by MCMC-based methods while being more than 100 times more efficient, showcasing the efficiency of our neural sampler. Besides the theoretical contributions and strong empirical performances, the proposed neural samplers and corresponding training methods will shed light on further research on developing efficient samplers for various applications beyond the ones explored in this study.

We introduce a novel grid-independent model for learning partial differential equations (PDEs) from noisy and partial observations on irregular spatiotemporal grids. We propose a space-time continuous latent neural PDE model with an efficient probabilistic framework and a novel encoder design for improved data efficiency and grid independence. The latent state dynamics are governed by a PDE model that combines the collocation method and the method of lines. We employ amortized variational inference for approximate posterior estimation and utilize a multiple shooting technique for enhanced training speed and stability. Our model demonstrates state-of-the-art performance on complex synthetic and real-world datasets, overcoming limitations of previous approaches and effectively handling partially-observed data. The proposed model outperforms recent methods, showing its potential to advance data-driven PDE modeling and enabling robust, grid-independent modeling of complex partially-observed dynamic processes across various domains.

Generalized Additive Models (GAMs) have recently experienced a resurgence in popularity due to their interpretability, which arises from expressing the target value as a sum of non-linear transformations of the features. Despite the current enthusiasm for GAMs, their susceptibility to concurvity — i.e., (possibly non-linear) dependencies between the features — has hitherto been largely overlooked. Here, we demonstrate how concurvity can severly impair the interpretability of GAMs and propose a remedy: a conceptually simple, yet effective regularizer which penalizes pairwise correlations of the non-linearly transformed feature variables. This procedure is applicable to any differentiable additive model, such as Neural Additive Models or NeuralProphet, and enhances interpretability by eliminating ambiguities due to self-canceling feature contributions. We validate the effectiveness of our regularizer in experiments on synthetic as well as real-world datasets for time-series and tabular data. Our experiments show that concurvity in GAMs can be reduced without significantly compromising prediction quality, improving interpretability and reducing variance in the feature importances.

Denoising diffusion models have proven to be a flexible and effective paradigm for generative modelling. Their recent extension to infinite dimensional Euclidean spaces has allowed for the modelling of stochastic processes. However, many problems in the natural sciences incorporate symmetries and involve data living in non-Euclidean spaces. In this work, we extend the framework of diffusion models to incorporate a series of geometric priors in infinite-dimension modelling. We do so by a) constructing a noising process which admits, as limiting distribution, a geometric Gaussian process that transforms under the symmetry group of interest, and b) approximating the score with a neural network that is equivariant w.r.t. this group. We show that with these conditions, the generative functional model admits the same symmetry. We demonstrate scalability and capacity of the model, using a novel Langevin-based conditional sampler, to fit complex scalar and vector fields, with Euclidean and spherical codomain, on synthetic and real-world weather data.

Decision-making in personalized medicine such as cancer therapy or critical care must often make choices for dosage combinations, i.e., multiple continuous treatments. Existing work for this task has modeled the effect of multiple treatments independently, while estimating the joint effect has received little attention but comes with non-trivial challenges. In this paper, we propose a novel method for reliable off-policy learning for dosage combinations. Our method proceeds along three steps: (1) We develop a tailored neural network that estimates the individualized dose-response function while accounting for the joint effect of multiple dependent dosages. (2) We estimate the generalized propensity score using conditional normalizing flows in order to detect regions with limited overlap in the shared covariate-treatment space. (3) We present a gradient-based learning algorithm to find the optimal, individualized dosage combinations. Here, we ensure reliable estimation of the policy value by avoiding regions with limited overlap. We finally perform an extensive evaluation of our method to show its effectiveness. To the best of our knowledge, ours is the first work to provide a method for reliable off-policy learning for optimal dosage combinations.

Impactful applications such as materials discovery, hardware design, neural architecture search, or portfolio optimization require optimizing high-dimensional black-box functions with mixed and combinatorial input spaces. While Bayesian optimization has recently made significant progress in solving such problems, an in-depth analysis reveals that the current state-of-the-art methods are not reliable. Their performances degrade substantially when the unknown optima of the function do not have a certain structure. To fill the need for a reliable algorithm for combinatorial and mixed spaces, this paper proposes Bounce that relies on a novel map of various variable types into nested embeddings of increasing dimensionality. Comprehensive experiments show that Bounce reliably achieves and often even improves upon state-of-the-art performance on a variety of high-dimensional problems.

Autoregressive neural networks within the temporal point process (TPP) framework have become the standard for modeling continuous-time event data. Even though these models can expressively capture event sequences in a one-step-ahead fashion, they are inherently limited for long-term forecasting applications due to the accumulation of errors caused by their sequential nature. To overcome these limitations, we derive ADD-THIN, a principled probabilistic denoising diffusion model for TPPs that operates on entire event sequences. Unlike existing diffusion approaches, ADD-THIN naturally handles data with discrete and continuous components. In experiments on synthetic and real-world datasets, our model matches the state-of-the-art TPP models in density estimation and strongly outperforms them in forecasting.

When learning simulations for modeling physical phenomena in industrial designs, geometrical variabilities are of prime interest. While classical regression techniques prove effective for parameterized geometries, practical scenarios often involve the absence of shape parametrization during the inference stage, leaving us with only mesh discretizations as available data. Learning simulations from such mesh-based representations poses significant challenges, with recent advances relying heavily on deep graph neural networks to overcome the limitations of conventional machine learning approaches. Despite their promising results, graph neural networks exhibit certain drawbacks, including their dependency on extensive datasets and limitations in providing built-in predictive uncertainties or handling large meshes. In this work, we propose a machine learning method that do not rely on graph neural networks. Complex geometrical shapes and variations with fixed topology are dealt with using well-known mesh morphing onto a common support, combined with classical dimensionality reduction techniques and Gaussian processes. The proposed methodology can easily deal with large meshes without the need for explicit shape parameterization and provides crucial predictive uncertainties, which are essential for informed decision-making. In the considered numerical experiments, the proposed method is competitive with respect to existing graph neural networks, regarding training efficiency and accuracy of the predictions.

Neural spiking activity is generally variable, non-stationary, and exhibits complex dependencies on covariates, such as sensory input or behavior. These dependencies have been proposed to be signatures of specific computations, and so characterizing them with quantitative rigor is critical for understanding neural computations. Approaches based on point processes provide a principled statistical framework for modeling neural spiking activity. However, currently, they only allow the instantaneous mean, but not the instantaneous variability, of responses to depend on covariates. To resolve this limitation, we propose a scalable Bayesian approach generalizing modulated renewal processes using sparse variational Gaussian processes. We leverage pathwise conditioning for computing nonparametric priors over conditional interspike interval distributions and rely on automatic relevance determination to detect lagging interspike interval dependencies beyond renewal order. After systematically validating our method on synthetic data, we apply it to two foundational datasets of animal navigation: head direction cells in freely moving mice and hippocampal place cells in rats running along a linear track. Our model exhibits competitive or better predictive power compared to state-of-the-art baselines, and outperforms them in terms of capturing interspike interval statistics. These results confirm the importance of modeling covariate-dependent spiking variability, and further analyses of our fitted models reveal rich patterns of variability modulation beyond the temporal resolution of flexible count-based approaches.

Many recent works in simulation-based inference (SBI) rely on deep generative models to approximate complex, high-dimensional posterior distributions. However, evaluating whether or not these approximations can be trusted remains a challenge. Most approaches evaluate the posterior estimator only in expectation over the observation space. This limits their interpretability and is not sufficient to identify for which observations the approximation can be trusted or should be improved. Building upon the well-known classifier two-sample test (C2ST), we introduce $\ell$-C2ST, a new method that allows for a local evaluation of the posterior estimator at any given observation. It offers theoretically grounded and easy to interpret -- e.g. graphical -- diagnostics, and unlike C2ST, does not require access to samples from the true posterior. In the case of normalizing flow-based posterior estimators, $\ell$-C2ST can be specialized to offer better statistical power, while being computationally more efficient. On standard SBI benchmarks, $\ell$-C2ST provides comparable results to C2ST and outperforms alternative local approaches such as coverage tests based on highest predictive density (HPD). We further highlight the importance of local evaluation and the benefit of interpretability of $\ell$-C2ST on a challenging application from computational neuroscience.

In this paper, we present continuous parametric optical flow, a parametric representation of dense and continuous motion over arbitrary time interval. In contrast to existing discrete-time representations (i.e., flow in between consecutive frames), this new representation transforms the frame-to-frame pixel correspondences to dense continuous flow. In particular, we present a temporal-parametric model that employs B-splines to fit point trajectories using a limited number of frames. To further improve the stability and robustness of the trajectories, we also add an encoder with a neural ordinary differential equation (ODE) to represent features associated with specific times. We also contribute a synthetic dataset and introduce two evaluation perspectives to measure the accuracy and robustness of continuous flow estimation. Benefiting from the combination of explicit parametric modeling and implicit feature optimization, our model focuses on motion continuity and outperforms than the flow-based and point-tracking approaches for fitting long-term and variable sequences.

Inference and simulation in the context of high-dimensional dynamical systems remain computationally challenging problems. Some form of dimensionality reduction is required to make the problem tractable in general. In this paper, we propose a novel approximate Gaussian filtering and smoothing method which propagates low-rank approximations of the covariance matrices. This is accomplished by projecting the Lyapunov equations associated with the prediction step to a manifold of low-rank matrices, which are then solved by a recently developed, numerically stable, dynamical low-rank integrator. Meanwhile, the update steps are made tractable by noting that the covariance update only transforms the column space of the covariance matrix, which is low-rank by construction. The algorithm differentiates itself from existing ensemble-based approaches in that the low-rank approximations of the covariance matrices are deterministic, rather than stochastic. Crucially, this enables the method to reproduce the exact Kalman filter as the low-rank dimension approaches the true dimensionality of the problem. Our method reduces computational complexity from cubic (for the Kalman filter) to quadratic in the state-space size in the worst-case, and can achieve linear complexity if the state-space model satisfies certain criteria. Through a set of experiments in classical data-assimilation and spatio-temporal regression, we show that the proposed method consistently outperforms the ensemble-based methods in terms of error in the mean and covariance with respect to the exact Kalman filter. This comes at no additional cost in terms of asymptotic computational complexity.

Exact inference of marginals in probabilistic graphical models (PGM) is known to be intractable, necessitating the use of approximate methods. Most of the existing variational techniques perform iterative message passing in loopy graphs which is slow to converge for many benchmarks. In this paper, we propose a new algorithm for marginal inference that is based on the incremental build-infer-approximate (IBIA) paradigm. Our algorithm converts the PGM into a sequence of linked clique tree forests (SLCTF) with bounded clique sizes, and then uses a heuristic belief update algorithm to infer the marginals. For the special case of Bayesian networks, we show that if the incremental build step in IBIA uses the topological order of variables then (a) the prior marginals are consistent in all CTFs in the SLCTF and (b) the posterior marginals are consistent once all evidence variables are added to the SLCTF. In our approach, the belief propagation step is non-iterative and the accuracy-complexity trade-off is controlled using user-defined clique size bounds. Results for several benchmark sets from recent UAI competitions show that our method gives either better or comparable accuracy than existing variational and sampling based methods, with smaller runtimes.

In this paper, we propose Barrier Hamiltonian Monte Carlo (BHMC), a version of the HMC algorithm which aims at sampling from a Gibbs distribution $\pi$ on a manifold $\mathsf{M}$, endowed with a Hessian metric $\mathfrak{g}$ derived from a self-concordant barrier. Our method relies on Hamiltonian dynamics which comprises $\mathfrak{g}$. Therefore, it incorporates the constraints defining $\mathsf{M}$ and is able to exploit its underlying geometry. However, the corresponding Hamiltonian dynamics is defined via non separable Ordinary Differential Equations (ODEs) in contrast to the Euclidean case. It implies unavoidable bias in existing generalization of HMC to Riemannian manifolds. In this paper, we propose a new filter step, called ``involution checking step'', to address this problem. This step is implemented in two versions of BHMC, coined continuous BHMC (c-bHMC) and numerical BHMC (n-BHMC) respectively. Our main results establish that these two new algorithms generate reversible Markov chains with respect to $\pi$ and do not suffer from any bias in comparison to previous implementations. Our conclusions are supported by numerical experiments where we consider target distributions defined on polytopes.

Optimal Transport (OT) problem investigates a transport map that bridges two distributions while minimizing a given cost function. In this regard, OT between tractable prior distribution and data has been utilized for generative modeling tasks. However, OT-based methods are susceptible to outliers and face optimization challenges during training. In this paper, we propose a novel generative model based on the semi-dual formulation of Unbalanced Optimal Transport (UOT). Unlike OT, UOT relaxes the hard constraint on distribution matching. This approach provides better robustness against outliers, stability during training, and faster convergence. We validate these properties empirically through experiments. Moreover, we study the theoretical upper-bound of divergence between distributions in UOT. Our model outperforms existing OT-based generative models, achieving FID scores of 2.97 on CIFAR-10 and 5.80 on CelebA-HQ-256. The code is available at \url{https://github.com/Jae-Moo/UOTM}.

In this study, we propose a novel deep spatio-temporal point process model, Deep Kernel Mixture Point Processes (DKMPP), that incorporates multimodal covariate information. DKMPP is an enhanced version of Deep Mixture Point Processes (DMPP), which uses a more flexible deep kernel to model complex relationships between events and covariate data, improving the model's expressiveness. To address the intractable training procedure of DKMPP due to the non-integrable deep kernel, we utilize an integration-free method based on score matching, and further improve efficiency by adopting a scalable denoising score matching method. Our experiments demonstrate that DKMPP and its corresponding score-based estimators outperform baseline models, showcasing the advantages of incorporating covariate information, utilizing a deep kernel, and employing score-based estimators.

Generative Flow Networks (GFlowNets), a class of generative models over discrete and structured sample spaces, have been previously applied to the problem of inferring the marginal posterior distribution over the directed acyclic graph (DAG) of a Bayesian Network, given a dataset of observations. Based on recent advances extending this framework to non-discrete sample spaces, we propose in this paper to approximate the joint posterior over not only the structure of a Bayesian Network, but also the parameters of its conditional probability distributions. We use a single GFlowNet whose sampling policy follows a two-phase process: the DAG is first generated sequentially one edge at a time, and then the corresponding parameters are picked once the full structure is known. Since the parameters are included in the posterior distribution, this leaves more flexibility for the local probability models of the Bayesian Network, making our approach applicable even to non-linear models parametrized by neural networks. We show that our method, called JSP-GFN, offers an accurate approximation of the joint posterior, while comparing favorably against existing methods on both simulated and real data.

To quantify uncertainty, conformal prediction methods are gaining continuously more interest and have already been successfully applied to various domains. However, they are difficult to apply to time series as the autocorrelative structure of time series violates basic assumptions required by conformal prediction. We propose HopCPT, a novel conformal prediction approach for time series that not only copes with temporal structures but leverages them. We show that our approach is theoretically well justified for time series where temporal dependencies are present. In experiments, we demonstrate that our new approach outperforms state-of-the-art conformal prediction methods on multiple real-world time series datasets from four different domains.

Particle-based variational inference methods (ParVIs) such as Stein variational gradient descent (SVGD) update the particles based on the kernelized Wasserstein gradient flow for the Kullback-Leibler (KL) divergence. However, the design of kernels is often non-trivial and can be restrictive for the flexibility of the method. Recent works show that functional gradient flow approximations with quadratic form regularization terms can improve performance. In this paper, we propose a ParVI framework, called generalized Wasserstein gradient descent (GWG), based on a generalized Wasserstein gradient flow of the KL divergence, which can be viewed as a functional gradient method with a broader class of regularizers induced by convex functions. We show that GWG exhibits strong convergence guarantees. We also provide an adaptive version that automatically chooses Wasserstein metric to accelerate convergence. In experiments, we demonstrate the effectiveness and efficiency of the proposed framework on both simulated and real data problems.

Large datasets are often affected by cell-wise outliers in the form of missing or erroneous data. However, discarding any samples containing outliers may result in a dataset that is too small to accurately estimate the covariance matrix. Moreover, the robust procedures designed to address this problem require the invertibility of the covariance operator and thus are not effective on high-dimensional data. In this paper, we propose an unbiased estimator for the covariance in the presence of missing values that does not require any imputation step and still achieves near minimax statistical accuracy with the operator norm. We also advocate for its use in combination with cell-wise outlier detection methods to tackle cell-wise contamination in a high-dimensional and low-rank setting, where state-of-the-art methods may suffer from numerical instability and long computation times. To complement our theoretical findings, we conducted an experimental study which demonstrates the superiority of our approach over the state of the art both in low and high dimension settings.

Probabilistic principal component analysis (PPCA) is currently one of the most used statistical tools to reduce the ambient dimension of the data. From multidimensional scaling to the imputation of missing data, PPCA has a broad spectrum of applications ranging from science and engineering to quantitative finance.\\ Despite this wide applicability in various fields, hardly any theoretical guarantees exist to justify the soundness of the maximal likelihood (ML) solution for this model. In fact, it is well known that the maximum likelihood estimation (MLE) can only recover the true model parameters up to a rotation. The main obstruction is posed by the inherent identifiability nature of the PPCA model resulting from the rotational symmetry of the parameterization. To resolve this ambiguity, we propose a novel approach using quotient topological spaces and in particular, we show that the maximum likelihood solution is consistent in an appropriate quotient Euclidean space. Furthermore, our consistency results encompass a more general class of estimators beyond the MLE. Strong consistency of the ML estimate and consequently strong covariance estimation of the PPCA model have also been established under a compactness assumption.

Bayesian Neural Networks (BNNs) provide a probabilistic interpretation for deep learning models by imposing a prior distribution over model parameters and inferring a posterior distribution based on observed data. The model sampled from the posterior distribution can be used for providing ensemble predictions and quantifying prediction uncertainty. It is well-known that deep learning models with lower sharpness have better generalization ability. However, existing posterior inferences are not aware of sharpness/flatness in terms of formulation, possibly leading to high sharpness for the models sampled from them. In this paper, we develop theories, the Bayesian setting, and the variational inference approach for the sharpness-aware posterior. Specifically, the models sampled from our sharpness-aware posterior, and the optimal approximate posterior estimating this sharpness-aware posterior, have better flatness, hence possibly possessing higher generalization ability. We conduct experiments by leveraging the sharpness-aware posterior with state-of-the-art Bayesian Neural Networks, showing that the flat-seeking counterparts outperform their baselines in all metrics of interest.

Langevin Monte Carlo (LMC) and its stochastic gradient versions are powerful algorithms for sampling from complex high-dimensional distributions. To sample from a distribution with density $\pi(\theta)\propto \exp(-U(\theta)) $, LMC iteratively generates the next sample by taking a step in the gradient direction $\nabla U$ with added Gaussian perturbations. Expectations w.r.t. the target distribution $\pi$ are estimated by averaging over LMC samples. In ordinary Monte Carlo, it is well known that the estimation error can be substantially reduced by replacing independent random samples by quasi-random samples like low-discrepancy sequences. In this work, we show that the estimation error of LMC can also be reduced by using quasi-random samples. Specifically, we propose to use completely uniformly distributed (CUD) sequences with certain low-discrepancy property to generate the Gaussian perturbations. Under smoothness and convexity conditions, we prove that LMC with a low-discrepancy CUD sequence achieves smaller error than standard LMC. The theoretical analysis is supported by compelling numerical experiments, which demonstrate the effectiveness of our approach.

The differential equation (DE) approach for convex optimization, which relates optimization methods to specific continuous DEs with rate-revealing Lyapunov functionals, has gained increasing interest since the seminal paper by Su--Boyd--Candès (2014). However, the approach still lacks a crucial component to make it truly useful: there is no general, consistent way to transition back to discrete optimization methods. Consequently, even if we derive insights from continuous DEs, we still need to perform individualized and tedious calculations for the analysis of each method. This paper aims to bridge this gap by introducing a new concept called ``weak discrete gradient'' (wDG), which consolidates the conditions required for discrete versions of gradients in the DE approach arguments. We then define abstract optimization methods using wDG and provide abstract convergence theories that parallel those in continuous DEs. We demonstrate that many typical optimization methods and their convergence rates can be derived as special cases of this abstract theory. The proposed unified discretization framework for the differential equation approach to convex optimization provides an easy environment for developing new optimization methods and achieving competitive convergence rates with state-of-the-art methods, such as Nesterov's accelerated gradient.

The diffusion model has shown remarkable success in computer vision, but it remains unclear whether the ODE-based probability flow or the SDE-based diffusion model is more superior and under what circumstances. Comparing the two is challenging due to dependencies on data distributions, score training, and other numerical issues. In this paper, we study the problem mathematically for two limiting scenarios: the zero diffusion (ODE) case and the large diffusion case. We first introduce a pulse-shape error to perturb the score function and analyze error accumulation of sampling quality, followed by a thorough analysis for generalization to arbitrary error. Our findings indicate that when the perturbation occurs at the end of the generative process, the ODE model outperforms the SDE model with a large diffusion coefficient. However, when the perturbation occurs earlier, the SDE model outperforms the ODE model. We demonstrate that the error of sample generation due to the pulse-shape perturbation is exponentially suppressed as the diffusion term's magnitude increases to infinity. Numerical validation of this phenomenon is provided using Gaussian, Gaussian mixture, and Swiss roll distribution, as well as realistic datasets like MNIST and CIFAR-10.

Fr\'echet regression has emerged as a promising approach for regression analysis involving non-Euclidean response variables. However, its practical applicability has been hindered by its reliance on ideal scenarios with abundant and noiseless covariate data. In this paper, we present a novel estimation method that tackles these limitations by leveraging the low-rank structure inherent in the covariate matrix. Our proposed framework combines the concepts of global Fr\'echet regression and principal component regression, aiming to improve the efficiency and accuracy of the regression estimator. By incorporating the low-rank structure, our method enables more effective modeling and estimation, particularly in high-dimensional and errors-in-variables regression settings. We provide a theoretical analysis of the proposed estimator's large-sample properties, including a comprehensive rate analysis of bias, variance, and additional variations due to measurement errors. Furthermore, our numerical experiments provide empirical evidence that supports the theoretical findings, demonstrating the superior performance of our approach. Overall, this work introduces a promising framework for regression analysis of non-Euclidean variables, effectively addressing the challenges associated with limited and noisy covariate data, with potential applications in diverse fields.

Semi-implicit variational inference (SIVI) has been introduced to expand the analytical variational families by defining expressive semi-implicit distributions in a hierarchical manner. However, the single-layer architecture commonly used in current SIVI methods can be insufficient when the target posterior has complicated structures. In this paper, we propose hierarchical semi-implicit variational inference, called HSIVI, which generalizes SIVI to allow more expressive multi-layer construction of semi-implicit distributions. By introducing auxiliary distributions that interpolate between a simple base distribution and the target distribution, the conditional layers can be trained by progressively matching these auxiliary distributions one layer after another. Moreover, given pre-trained score networks, HSIVI can be used to accelerate the sampling process of diffusion models with the score matching objective. We show that HSIVI significantly enhances the expressiveness of SIVI on several Bayesian inference problems with complicated target distributions. When used for diffusion model acceleration, we show that HSIVI can produce high quality samples comparable to or better than the existing fast diffusion model based samplers with a small number of function evaluations on various datasets.

Recently, diffusion models have achieved great success in generative tasks. Sampling from diffusion models is equivalent to solving the reverse diffusion stochastic differential equations (SDEs) or the corresponding probability flow ordinary differential equations (ODEs). In comparison, SDE-based solvers can generate samples of higher quality and are suited for image translation tasks like stroke-based synthesis. During inference, however, existing SDE-based solvers are severely constrained by the efficiency-effectiveness dilemma. Our investigation suggests that this is because the Gaussian assumption in the reverse transition kernel is frequently violated (even in the case of simple mixture data) given a limited number of discretization steps. To overcome this limitation, we introduce a novel class of SDE-based solvers called \emph{Gaussian Mixture Solvers (GMS)} for diffusion models. Our solver estimates the first three-order moments and optimizes the parameters of a Gaussian mixture transition kernel using generalized methods of moments in each step during sampling. Empirically, our solver outperforms numerous SDE-based solvers in terms of sample quality in image generation and stroke-based synthesis in various diffusion models, which validates the motivation and effectiveness of GMS. Our code is available at https://github.com/Guohanzhong/GMS.

We propose a Gaussian manifold variational auto-encoder (GM-VAE) whose latent space consists of a set of Gaussian distributions. It is known that the set of the univariate Gaussian distributions with the Fisher information metric form a hyperbolic space, which we call a Gaussian manifold. To learn the VAE endowed with the Gaussian manifolds, we propose a pseudo-Gaussian manifold normal distribution based on the Kullback-Leibler divergence, a local approximation of the squared Fisher-Rao distance, to define a density over the latent space. We demonstrate the efficacy of GM-VAE on two different tasks: density estimation of image datasets and state representation learning for model-based reinforcement learning. GM-VAE outperforms the other variants of hyperbolic- and Euclidean-VAEs on density estimation tasks and shows competitive performance in model-based reinforcement learning. We observe that our model provides strong numerical stability, addressing a common limitation reported in previous hyperbolic-VAEs. The implementation is available at https://github.com/ml-postech/GM-VAE.

We provide the first polynomial-time convergence guarantees for the probabilistic flow ODE implementation (together with a corrector step) of score-based generative modeling. Our analysis is carried out in the wake of recent results obtaining such guarantees for the SDE-based implementation (i.e., denoising diffusion probabilistic modeling or DDPM), but requires the development of novel techniques for studying deterministic dynamics without contractivity. Through the use of a specially chosen corrector step based on the underdamped Langevin diffusion, we obtain better dimension dependence than prior works on DDPM ($O(\sqrt d)$ vs. $O(d)$, assuming smoothness of the data distribution), highlighting potential advantages of the ODE framework.

Recently, diffusion probabilistic models (DPMs) have achieved promising results in diverse generative tasks. A typical DPM framework includes a forward process that gradually diffuses the data distribution and a reverse process that recovers the data distribution from time-dependent data scores. In this work, we observe that the stochastic reverse process of data scores is a martingale, from which concentration bounds and the optional stopping theorem for data scores can be derived. Then, we discover a simple way for calibrating an arbitrary pretrained DPM, with which the score matching loss can be reduced and the lower bounds of model likelihood can consequently be increased. We provide general calibration guidelines under various model parametrizations. Our calibration method is performed only once and the resulting models can be used repeatedly for sampling. We conduct experiments on multiple datasets to empirically validate our proposal. Our code is available at https://github.com/thudzj/Calibrated-DPMs.

Measuring the nonlinear dependence between random vectors and testing for their statistical independence is a fundamental problem in statistics. One of the most popular dependence measures is the Hilbert-Schmidt independence criterion (HSIC), which has attracted increasing attention in recent years. However, most existing works have focused on either fixed or very high-dimensional covariates. In this work, we bridge the gap between these two scenarios and provide statistical insights into the performance of HSIC when the dimensions grow at different rates. We first show that, under the null hypothesis, the rescaled HSIC converges in distribution to a standard normal distribution. Then we provide a general condition for the HSIC based tests to have nontrivial power in high dimensions. By decomposing this condition, we illustrate how the ability of HSIC to measure nonlinear dependence changes with increasing dimensions. Moreover, we demonstrate that, depending on the sample size, the covariate dimensions and the dependence structures within covariates, the HSIC can capture different types of associations between random vectors. We also conduct extensive numerical studies to validate our theoretical results.

This paper investigates the asymptotic distribution of the maximum-likelihood estimate (MLE) in multinomial logistic models in the high-dimensional regime where dimension and sample size are of the same order. While classical large-sample theory provides asymptotic normality of the MLE under certain conditions, such classical results are expected to fail in high-dimensions as documented for the binary logistic case in the seminal work of Sur and Candès [2019]. We address this issue in classification problems with 3 or more classes, by developing asymptotic normality and asymptotic chi-square results for the multinomial logistic MLE (also known as cross-entropy minimizer) on null covariates. Our theory leads to a new methodology to test the significance of a given feature. Extensive simulation studies on synthetic data corroborate these asymptotic results and confirm the validity of proposed p-values for testing the significance of a given feature.

Many practical settings call for the reconstruction of temporal signals from corrupted or missing data. Classic examples include decoding, tracking, signal enhancement and denoising. Since the reconstructed signals are ultimately viewed by humans, it is desirable to achieve reconstructions that are pleasing to human perception. Mathematically, perfect perceptual-quality is achieved when the distribution of restored signals is the same as that of natural signals, a requirement which has been heavily researched in static estimation settings (i.e. when a whole signal is processed at once). Here, we study the problem of optimal causal filtering under a perfect perceptual-quality constraint, which is a task of fundamentally different nature. Specifically, we analyze a Gaussian Markov signal observed through a linear noisy transformation. In the absence of perceptual constraints, the Kalman filter is known to be optimal in the MSE sense for this setting. Here, we show that adding the perfect perceptual quality constraint (i.e. the requirement of temporal consistency), introduces a fundamental dilemma whereby the filter may have to ``knowingly'' ignore new information revealed by the observations in order to conform to its past decisions. This often comes at the cost of a significant increase in the MSE (beyond that encountered in static settings). Our analysis goes beyond the classic innovation process of the Kalman filter, and introduces the novel concept of an unutilized information process. Using this tool, we present a recursive formula for perceptual filters, and demonstrate the qualitative effects of perfect perceptual-quality estimation on a video reconstruction problem.

In this paper, we present conditions for identifying the generator of a linear stochastic differential equation (SDE) from the distribution of its solution process with a given fixed initial state. These identifiability conditions are crucial in causal inference using linear SDEs as they enable the identification of the post-intervention distributions from its observational distribution. Specifically, we derive a sufficient and necessary condition for identifying the generator of linear SDEs with additive noise, as well as a sufficient condition for identifying the generator of linear SDEs with multiplicative noise. We show that the conditions derived for both types of SDEs are generic. Moreover, we offer geometric interpretations of the derived identifiability conditions to enhance their understanding. To validate our theoretical results, we perform a series of simulations, which support and substantiate the established findings.

Projection robust Wasserstein (PRW) distance is recently proposed to efficiently mitigate the curse of dimensionality in the classical Wasserstein distance. In this paper, by equivalently reformulating the computation of the PRW distance as an optimization problem over the Cartesian product of the Stiefel manifold and the Euclidean space with additional nonlinear inequality constraints, we propose a Riemannian exponential augmented Lagrangian method (REALM) for solving this problem. Compared with the existing Riemannian exponential penalty-based approaches, REALM can potentially avoid too small penalty parameters and exhibit more stable numerical performance. To solve the subproblems in REALM efficiently, we design an inexact Riemannian Barzilai-Borwein method with Sinkhorn iteration (iRBBS), which selects the stepsizes adaptively rather than tuning the stepsizes in efforts as done in the existing methods. We show that iRBBS can return an $\epsilon$-stationary point of the original PRW distance problem within $\mathcal{O}(\epsilon^{-3})$ iterations, which matches the best known iteration complexity result. Extensive numerical results demonstrate that our proposed methods outperform the state-of-the-art solvers for computing the PRW distance.

Unrolled computation graphs are prevalent throughout machine learning but present challenges to automatic differentiation (AD) gradient estimation methods when their loss functions exhibit extreme local sensitivtiy, discontinuity, or blackbox characteristics. In such scenarios, online evolution strategies methods are a more capable alternative, while being more parallelizable than vanilla evolution strategies (ES) by interleaving partial unrolls and gradient updates. In this work, we propose a general class of unbiased online evolution strategies methods. We analytically and empirically characterize the variance of this class of gradient estimators and identify the one with the least variance, which we term Noise-Reuse Evolution Strategies (NRES). Experimentally, we show NRES results in faster convergence than existing AD and ES methods in terms of wall-clock time and number of unroll steps across a variety of applications, including learning dynamical systems, meta-training learned optimizers, and reinforcement learning.

Many machine learning approaches for decision making, such as reinforcement learning, rely on simulators or predictive models to forecast the time-evolution of quantities of interest, e.g., the state of an agent or the reward of a policy. Forecasts of such complex phenomena are commonly described by highly nonlinear dynamical systems, making their use in optimization-based decision-making challenging. Koopman operator theory offers a beneficial paradigm for addressing this problem by characterizing forecasts via linear time-invariant (LTI) ODEs -- turning multi-step forecasting into sparse matrix multiplications. Though there exists a variety of learning approaches, they usually lack crucial learning-theoretic guarantees, making the behavior of the obtained models with increasing data and dimensionality unclear. We address the aforementioned by deriving a novel reproducing kernel Hilbert space (RKHS) over trajectories that solely spans transformations into LTI dynamical systems. The resulting Koopman Kernel Regression (KKR) framework enables the use of statistical learning tools from function approximation for novel convergence results and generalization error bounds under weaker assumptions than existing work. Our experiments demonstrate superior forecasting performance compared to Koopman operator and sequential data predictors in RKHS.

Causal effect estimation from data typically requires assumptions about the cause-effect relations either explicitly in the form of a causal graph structure within the Pearlian framework, or implicitly in terms of (conditional) independence statements between counterfactual variables within the potential outcomes framework. When the treatment variable and the outcome variable are confounded, front-door adjustment is an important special case where, given the graph, causal effect of the treatment on the target can be estimated using post-treatment variables. However, the exact formula for front-door adjustment depends on the structure of the graph, which is difficult to learn in practice. In this work, we provide testable conditional independence statements to compute the causal effect using front-door-like adjustment without knowing the graph under limited structural side information. We show that our method is applicable in scenarios where knowing the Markov equivalence class is not sufficient for causal effect estimation. We demonstrate the effectiveness of our method on a class of random graphs as well as real causal fairness benchmarks.

Data-driven machine learning approaches are being increasingly used to solve partial differential equations (PDEs). They have shown particularly striking successes when training an operator, which takes as input a PDE in some family, and outputs its solution. However, the architectural design space, especially given structural knowledge of the PDE family of interest, is still poorly understood. We seek to remedy this gap by studying the benefits of weight-tied neural network architectures for steady-state PDEs. To achieve this, we first demonstrate that the solution of most steady-state PDEs can be expressed as a fixed point of a non-linear operator. Motivated by this observation, we propose FNO-DEQ, a deep equilibrium variant of the FNO architecture that directly solves for the solution of a steady-state PDE as the infinite-depth fixed point of an implicit operator layer using a black-box root solver and differentiates analytically through this fixed point resulting in $\mathcal{O}(1)$ training memory. Our experiments indicate that FNO-DEQ-based architectures outperform FNO-based baselines with $4\times$ the number of parameters in predicting the solution to steady-state PDEs such as Darcy Flow and steady-state incompressible Navier-Stokes. Finally, we show FNO-DEQ is more robust when trained with datasets with more noisy observations than the FNO-based baselines, demonstrating the benefits of using appropriate inductive biases in architectural design for different neural network based PDE solvers. Further, we show a universal approximation result that demonstrates that FNO-DEQ can approximate the solution to any steady-state PDE that can be written as a fixed point equation.

In reinforcement learning, robust policies for high-stakes decision-making problems with limited data are usually computed by optimizing the percentile criterion. The percentile criterion is optimized by constructing an uncertainty set that contains the true model with high probability and optimizing the policy for the worst model in the set. Since the percentile criterion is non-convex, constructing these sets itself is challenging. Existing works use Bayesian credible regions as uncertainty sets, but they are often unnecessarily large and result in learning overly conservative policies. To overcome these shortcomings, we propose a novel Value-at-Risk based dynamic programming algorithm to optimize the percentile criterion without explicitly constructing any uncertainty sets. Our theoretical and empirical results show that our algorithm implicitly constructs much smaller uncertainty sets and learns less-conservative robust policies.

In computational social science (CSS), researchers analyze documents to explain social and political phenomena. In most scenarios, CSS researchers first obtain labels for documents and then explain labels using interpretable regression analyses in the second step. One increasingly common way to annotate documents cheaply at scale is through large language models (LLMs). However, like other scalable ways of producing annotations, such surrogate labels are often imperfect and biased. We present a new algorithm for using imperfect annotation surrogates for downstream statistical analyses while guaranteeing statistical properties—like asymptotic unbiasedness and proper uncertainty quantification—which are fundamental to CSS research. We show that direct use of surrogate labels in downstream statistical analyses leads to substantial bias and invalid confidence intervals, even with high surrogate accuracy of 80-90\%. To address this, we build on debiased machine learning to propose the design-based supervised learning (DSL) estimator. DSL employs a doubly-robust procedure to combine surrogate labels with a smaller number of high-quality, gold-standard labels. Our approach guarantees valid inference for downstream statistical analyses, even when surrogates are arbitrarily biased and without requiring stringent assumptions, by controlling the probability of sampling documents for gold-standard labeling. Both our theoretical analysis and experimental results show that DSL provides valid statistical inference while achieving root mean squared errors comparable to existing alternatives that focus only on prediction without inferential guarantees.

We introduce Functional Diffusion Processes (FDPs), which generalize score-based diffusion models to infinite-dimensional function spaces. FDPs require a new mathematical framework to describe the forward and backward dynamics, and several extensions to derive practical training objectives. These include infinite-dimensional versions of Girsanov theorem, in order to be able to compute an ELBO, and of the sampling theorem, in order to guarantee that functional evaluations in a countable set of points are equivalent to infinite-dimensional functions. We use FDPs to build a new breed of generative models in function spaces, which do not require specialized network architectures, and that can work with any kind of continuous data. Our results on real data show that FDPs achieve high-quality image generation, using a simple MLP architecture with orders of magnitude fewer parameters than existing diffusion models.

We consider the problem of a revenue-maximizing seller with a large number of items $m$ for sale to $n$ strategic bidders, whose valuations are drawn independently from high-dimensional, unknown prior distributions. It is well-known that optimal and even approximately-optimal mechanisms for this setting are notoriously difficult to characterize or compute, and, even when they can be found, are often rife with various counter-intuitive properties. In this paper, following a model introduced recently by Cai and Daskalakis [CD22], we consider the case that bidders' prior distributions can be well-approximated by a topic model. We design an active learning component, responsible for interacting with the bidders and outputting low-dimensional approximations of their types, and a mechanism design component, responsible for robustifying mechanisms for the low-dimensional model to work for the approximate types of the former component. On the active learning front, we cast our problem in the framework of Randomized Linear Algebra (RLA) for regression problems, allowing us to import several breakthrough results from that line of research, and adapt them to our setting. On the mechanism design front, we remove many restrictive assumptions of prior work on the type of access needed to the underlying distributions and the associated mechanisms. To the best of our knowledge, our work is the first to formulate connections between mechanism design, and RLA for active learning of regression problems, opening the door for further applications of randomized linear algebra primitives to mechanism design.

Plug-and-play (PnP) prior is a well-known class of methods for solving imaging inverse problems by computing fixed-points of operators combining physical measurement models and learned image denoisers. While PnP methods have been extensively used for image recovery with known measurement operators, there is little work on PnP for solving blind inverse problems. We address this gap by presenting a new block-coordinate PnP (BC-PnP) method that efficiently solves this joint estimation problem by introducing learned denoisers as priors on both the unknown image and the unknown measurement operator. We present a new convergence theory for BC-PnP compatible with blind inverse problems by considering nonconvex data-fidelity terms and expansive denoisers. Our theory analyzes the convergence of BC-PnP to a stationary point of an implicit function associated with an approximate minimum mean-squared error (MMSE) denoiser. We numerically validate our method on two blind inverse problems: automatic coil sensitivity estimation in magnetic resonance imaging (MRI) and blind image deblurring. Our results show that BC-PnP provides an efficient and principled framework for using denoisers as PnP priors for jointly estimating measurement operators and images.

We present a discretization-free scalable framework for solving a large class of mass-conserving partial differential equations (PDEs), including the time-dependent Fokker-Planck equation and the Wasserstein gradient flow. The main observation is that the time-varying velocity field of the PDE solution needs to be self-consistent: it must satisfy a fixed-point equation involving the probability flow characterized by the same velocity field. Instead of directly minimizing the residual of the fixed-point equation with neural parameterization, we use an iterative formulation with a biased gradient estimator that bypasses significant computational obstacles with strong empirical performance. Compared to existing approaches, our method does not suffer from temporal or spatial discretization, covers a wider range of PDEs, and scales to high dimensions. Experimentally, our method recovers analytical solutions accurately when they are available and achieves superior performance in high dimensions with less training time compared to alternatives.

Mutual information is a general statistical dependency measure which has found applications in representation learning, causality, domain generalization and computational biology. However, mutual information estimators are typically evaluated on simple families of probability distributions, namely multivariate normal distribution and selected distributions with one-dimensional random variables. In this paper, we show how to construct a diverse family of distributions with known ground-truth mutual information and propose a language-independent benchmarking platform for mutual information estimators. We discuss the general applicability and limitations of classical and neural estimators in settings involving high dimensions, sparse interactions, long-tailed distributions, and high mutual information. Finally, we provide guidelines for practitioners on how to select appropriate estimator adapted to the difficulty of problem considered and issues one needs to consider when applying an estimator to a new data set.

Regularization is one of the most fundamental topics in optimization, statistics and machine learning. To get sparsity in estimating a parameter $u\in\mathbb{R}^d$, an $\ell_q$ penalty term, $\Vert u\Vert_q$, is usually added to the objective function. What is the probabilistic distribution corresponding to such $\ell_q$ penalty? What is the \emph{correct} stochastic process corresponding to $\Vert u\Vert_q$ when we model functions $u\in L^q$? This is important for statistically modeling high-dimensional objects such as images, with penalty to preserve certainty properties, e.g. edges in the image. In this work, we generalize the $q$-exponential distribution (with density proportional to) $\exp{(- \frac{1}{2}|u|^q)}$ to a stochastic process named \emph{$Q$-exponential (Q-EP) process} that corresponds to the $L_q$ regularization of functions. The key step is to specify consistent multivariate $q$-exponential distributions by choosing from a large family of elliptic contour distributions. The work is closely related to Besov process which is usually defined in terms of series. Q-EP can be regarded as a definition of Besov process with explicit probabilistic formulation, direct control on the correlation strength, and tractable prediction formula. From the Bayesian perspective, Q-EP provides a flexible prior on functions with sharper penalty ($q<2$) than the commonly used Gaussian process (GP, $q=2$). We compare GP, Besov and Q-EP in modeling functional data, reconstructing images and solving inverse problems and demonstrate the advantage of our proposed methodology.

This paper studies the fundamental learning problem of the energy-based model (EBM). Learning the EBM can be achieved using the maximum likelihood estimation (MLE), which typically involves the Markov Chain Monte Carlo (MCMC) sampling, such as the Langevin dynamics. However, the noise-initialized Langevin dynamics can be challenging in practice and hard to mix. This motivates the exploration of joint training with the generator model where the generator model serves as a complementary model to bypass MCMC sampling. However, such a method can be less accurate than the MCMC and result in biased EBM learning. While the generator can also serve as an initializer model for better MCMC sampling, its learning can be biased since it only matches the EBM and has no access to empirical training examples. Such biased generator learning may limit the potential of learning the EBM. To address this issue, we present a joint learning framework that interweaves the maximum likelihood learning algorithm for both the EBM and the complementary generator model. In particular, the generator model is learned by MLE to match both the EBM and the empirical data distribution, making it a more informative initializer for MCMC sampling of EBM. Learning generator with observed examples typically requires inference of the generator posterior. To ensure accurate and efficient inference, we adopt the MCMC posterior sampling and introduce a complementary inference model to initialize such latent MCMC sampling. We show that three separate models can be seamlessly integrated into our joint framework through two (dual-) MCMC teaching, enabling effective and efficient EBM learning.

Constraint-based causal discovery algorithms learn part of the causal graph structure by systematically testing conditional independences observed in the data. These algorithms, such as the PC algorithm and its variants, rely on graphical characterizations of the so-called equivalence class of causal graphs proposed by Pearl. However, constraint-based causal discovery algorithms struggle when data is limited since conditional independence tests quickly lose their statistical power, especially when the conditioning set is large. To address this, we propose using conditional independence tests where the size of the conditioning set is upper bounded by some integer k for robust causal discovery. The existing graphical characterizations of the equivalence classes of causal graphs are not applicable when we cannot leverage all the conditional independence statements. We first define the notion of k-Markov equivalence: Two causal graphs are k-Markov equivalent if they entail the same conditional independence constraints where the conditioning set size is upper bounded by k. We propose a novel representation that allows us to graphically characterize k-Markov equivalence between two causal graphs. We propose a sound constraint-based algorithm called the k-PC algorithm for learning this equivalence class. Finally, we conduct synthetic, and semi-synthetic experiments to demonstrate that the k-PC algorithm enables more robust causal discovery in the small sample regime compared to the baseline algorithms.

Inferring causal structure from data is a challenging task of fundamental importance in science. Often, observational data alone is not enough to uniquely identify a system’s causal structure. The use of interventional data can address this issue, however, acquiring these samples typically demands a considerable investment of time and physical or financial resources. In this work, we are concerned with the acquisition of interventional data in a targeted manner to minimize the number of required experiments. We propose a novel Gradient-based Intervention Targeting method, abbreviated GIT, that ’trusts’ the gradient estimator of a gradient-based causal discovery framework to provide signals for the intervention targeting function. We provide extensive experiments in simulated and real-world datasets and demonstrate that GIT performs on par with competitive baselines, surpassing them in the low-data regime.

Earth system forecasting has traditionally relied on complex physical models that are computationally expensive and require significant domain expertise. In the past decade, the unprecedented increase in spatiotemporal Earth observation data has enabled data-driven forecasting models using deep learning techniques. These models have shown promise for diverse Earth system forecasting tasks but either struggle with handling uncertainty or neglect domain-specific prior knowledge, resulting in averaging possible futures to blurred forecasts or generating physically implausible predictions. To address these limitations, we propose a two-stage pipeline for probabilistic spatiotemporal forecasting: 1) We develop *PreDiff*, a conditional latent diffusion model capable of probabilistic forecasts. 2) We incorporate an explicit knowledge alignment mechanism to align forecasts with domain-specific physical constraints. This is achieved by estimating the deviation from imposed constraints at each denoising step and adjusting the transition distribution accordingly. We conduct empirical studies on two datasets: N-body MNIST, a synthetic dataset with chaotic behavior, and SEVIR, a real-world precipitation nowcasting dataset. Specifically, we impose the law of conservation of energy in N-body MNIST and anticipated precipitation intensity in SEVIR. Experiments demonstrate the effectiveness of PreDiff in handling uncertainty, incorporating domain-specific prior knowledge, and generating forecasts that exhibit high operational utility.

Diffusion-based manifold learning methods have proven useful in representation learning and dimensionality reduction of modern high dimensional, high throughput, noisy datasets. Such datasets are especially present in fields like biology and physics. While it is thought that these methods preserve underlying manifold structure of data by learning a proxy for geodesic distances, no specific theoretical links have been established. Here, we establish such a link via results in Riemannian geometry explicitly connecting heat diffusion to manifold distances. In this process, we also formulate a more general heat kernel based manifold embedding method that we call heat geodesic embeddings. This novel perspective makes clearer the choices available in manifold learning and denoising. Results show that our method outperforms existing state of the art in preserving ground truth manifold distances, and preserving cluster structure in toy datasets. We also showcase our method on single cell RNA-sequencing datasets with both continuum and cluster structure, where our method enables interpolation of withheld timepoints of data. Finally, we show that parameters of our more general method can be configured to give results similar to PHATE (a state-of-the-art diffusion based manifold learning method) as well as SNE (an attraction/repulsion neighborhood based method that forms the basis of t-SNE).

We introduce a suite of new particle-based algorithms for sampling on constrained domains which are entirely learning rate free. Our approach leverages coin betting ideas from convex optimisation, and the viewpoint of constrained sampling as a mirrored optimisation problem on the space of probability measures. Based on this viewpoint, we also introduce a unifying framework for several existing constrained sampling algorithms, including mirrored Langevin dynamics and mirrored Stein variational gradient descent. We demonstrate the performance of our algorithms on a range of numerical examples, including sampling from targets on the simplex, sampling with fairness constraints, and constrained sampling problems in post-selection inference. Our results indicate that our algorithms achieve competitive performance with existing constrained sampling methods, without the need to tune any hyperparameters.

Machine learning for differential equations paves the way for computationally efficient alternatives to numerical solvers, with potentially broad impacts in science and engineering. Though current algorithms typically require simulated training data tailored to a given setting, one may instead wish to learn useful information from heterogeneous sources, or from real dynamical systems observations that are messy or incomplete. In this work, we learn general-purpose representations of PDEs from heterogeneous data by implementing joint embedding methods for self-supervised learning (SSL), a framework for unsupervised representation learning that has had notable success in computer vision. Our representation outperforms baseline approaches to invariant tasks, such as regressing the coefficients of a PDE, while also improving the time-stepping performance of neural solvers. We hope that our proposed methodology will prove useful in the eventual development of general-purpose foundation models for PDEs.

Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies and evolutionary distances on branches, is crucial for accurately inferring species relationships from molecular data and tasks requiring variable marginalization. Variational Bayesian methods are key to developing scalable, practical models; however, it remains challenging to conduct phylogenetic inference without restricting the combinatorially vast number of possible tree topologies. In this work, we introduce a novel, fully differentiable formulation of phylogenetic inference that leverages a unique representation of topological distributions in continuous geometric spaces. Through practical considerations on design spaces and control variates for gradient estimations, our approach, GeoPhy, enables variational inference without limiting the topological candidates. In experiments using real benchmark datasets, GeoPhy significantly outperformed other approximate Bayesian methods that considered whole topologies.

Plug-and-Play (PnP) methods are efficient iterative algorithms for solving ill-posed image inverse problems. PnP methods are obtained by using deep Gaussian denoisers instead of the proximal operator or the gradient-descent step within proximal algorithms. Current PnP schemes rely on data-fidelity terms that have either Lipschitz gradients or closed-form proximal operators, which is not applicable to Poisson inverse problems. Based on the observation that the Gaussian noise is not the adequate noise model in this setting, we propose to generalize PnP using the Bregman Proximal Gradient (BPG) method. BPG replaces the Euclidean distance with a Bregman divergence that can better capture the smoothness properties of the problem. We introduce the Bregman Score Denoiser specifically parametrized and trained for the new Bregman geometry and prove that it corresponds to the proximal operator of a nonconvex potential. We propose two PnP algorithms based on the Bregman Score Denoiser for solving Poisson inverse problems. Extending the convergence results of BPG in the nonconvex settings, we show that the proposed methods converge, targeting stationary points of an explicit global functional. Experimental evaluations conducted on various Poisson inverse problems validate the convergence results and showcase effective restoration performance.

Biases with respect to socially-salient attributes of individuals have been well documented in evaluation processes used in settings such as admissions and hiring. We view such an evaluation process as a transformation of a distribution of the true utility of an individual for a task to an observed distribution and model it as a solution to a loss minimization problem subject to an information constraint. Our model has two parameters that have been identified as factors leading to biases: the resource-information trade-off parameter in the information constraint and the risk-averseness parameter in the loss function. We characterize the distributions that arise from our model and study the effect of the parameters on the observed distribution. The outputs of our model enrich the class of distributions that can be used to capture variation across groups in the observed evaluations. We empirically validate our model by fitting real-world datasets and use it to study the effect of interventions in a downstream selection task. These results contribute to an understanding of the emergence of bias in evaluation processes and provide tools to guide the deployment of interventions to mitigate biases.

Bayesian inference allows expressing the uncertainty of posterior belief under a probabilistic model given prior information and the likelihood of the evidence. Predominantly, the likelihood function is only implicitly established by a simulator posing the need for simulation-based inference (SBI). However, the existing algorithms can yield overconfident posteriors (Hermans *et al.*, 2022) defeating the whole purpose of credibility if the uncertainty quantification is inaccurate. We propose to include a calibration term directly into the training objective of the neural model in selected amortized SBI techniques. By introducing a relaxation of the classical formulation of calibration error we enable end-to-end backpropagation. The proposed method is not tied to any particular neural model and brings moderate computational overhead compared to the profits it introduces. It is directly applicable to existing computational pipelines allowing reliable black-box posterior inference. We empirically show on six benchmark problems that the proposed method achieves competitive or better results in terms of coverage and expected posterior density than the previously existing approaches.

We study the problem of combining neural networks with symbolic reasoning. Recently introduced frameworks for Probabilistic Neurosymbolic Learning (PNL), such as DeepProbLog, perform exponential-time exact inference, limiting the scalability of PNL solutions. We introduce Approximate Neurosymbolic Inference (A-NeSI): a new framework for PNL that uses neural networks for scalable approximate inference. A-NeSI 1) performs approximate inference in polynomial time without changing the semantics of probabilistic logics; 2) is trained using data generated by the background knowledge; 3) can generate symbolic explanations of predictions; and 4) can guarantee the satisfaction of logical constraints at test time, which is vital in safety-critical applications. Our experiments show that A-NeSI is the first end-to-end method to solve three neurosymbolic tasks with exponential combinatorial scaling. Finally, our experiments show that A-NeSI achieves explainability and safety without a penalty in performance.

Classification is a fundamental problem in machine learning, and considerable efforts have been recently devoted to the demanding long-tailed setting due to its prevalence in nature. Departure from the Bayesian framework, this paper rethinks classification from a matching perspective by studying the matching probability between samples and labels with optimal transport (OT) formulation. Specifically, we first propose a new variant of optimal transport, called Relative Entropic Optimal Transport (RE-OT), which guides the coupling solution to a known prior information matrix. We gives some theoretical results and their proof for RE-OT and surprisingly find RE-OT can help to deblur for barycenter images. Then we adopt inverse RE-OT for training long-tailed data and find that the loss derived from RE-OT has a similar form to Softmax-based cross-entropy loss, indicating a close connection between optimal transport and classification and the potential for transferring concepts between these two academic fields, such as barycentric projection in OT, which can map the labels back to the feature space. We further derive an epoch-varying RE-OT loss, and do the experiments on unbalanced image classification, molecule classification, instance segmentation and representation learning. Experimental results show its effectiveness.

Wasserstein distributionally robust estimators have emerged as powerful models for prediction and decision-making under uncertainty. These estimators provide attractive generalization guarantees: the robust objective obtained from the training distribution is an exact upper bound on the true risk with high probability. However, existing guarantees either suffer from the curse of dimensionality, are restricted to specific settings, or lead to spurious error terms. In this paper, we show that these generalization guarantees actually hold on general classes of models, do not suffer from the curse of dimensionality, and can even cover distribution shifts at testing. We also prove that these results carry over to the newly-introduced regularized versions of Wasserstein distributionally robust problems.

Certifiable, adaptive uncertainty estimates for unknown quantities are an essential ingredient of sequential decision-making algorithms. Standard approaches rely on problem-dependent concentration results and are limited to a specific combination of parameterization, noise family, and estimator. In this paper, we revisit the likelihood-based inference principle and propose to use \emph{likelihood ratios} to construct \emph{any-time valid} confidence sequences without requiring specialized treatment in each application scenario. Our method is especially suitable for problems with well-specified likelihoods, and the resulting sets always maintain the prescribed coverage in a model-agnostic manner. The size of the sets depends on a choice of estimator sequence in the likelihood ratio. We discuss how to provably choose the best sequence of estimators and shed light on connections to online convex optimization with algorithms such as Follow-the-Regularized-Leader. To counteract the initially large bias of the estimators, we propose a reweighting scheme that also opens up deployment in non-parametric settings such as RKHS function classes. We provide a \emph{non-asymptotic} analysis of the likelihood ratio confidence sets size for generalized linear models, using insights from convex duality and online learning. We showcase the practical strength of our method on generalized linear bandit problems, survival analysis, and bandits with various additive noise distributions.

While deep learning techniques have become extremely popular for solving a broad range of optimization problems, methods to enforce hard constraints during optimization, particularly on deep neural networks, remain underdeveloped. Inspired by the rich literature on meshless interpolation and its extension to spectral collocation methods in scientific computing, we develop a series of approaches for enforcing hard constraints on neural fields, which we refer to as Constrained Neural Fields (CNF). The constraints can be specified as a linear operator applied to the neural field and its derivatives. We also design specific model representations and training strategies for problems where standard models may encounter difficulties, such as conditioning of the system, memory consumption, and capacity of the network when being constrained. Our approaches are demonstrated in a wide range of real-world applications. Additionally, we develop a framework that enables highly efficient model and constraint specification, which can be readily applied to any downstream task where hard constraints need to be explicitly satisfied during optimization.

Data assimilation, in its most comprehensive form, addresses the Bayesian inverse problem of identifying plausible state trajectories that explain noisy or incomplete observations of stochastic dynamical systems. Various approaches have been proposed to solve this problem, including particle-based and variational methods. However, most algorithms depend on the transition dynamics for inference, which becomes intractable for long time horizons or for high-dimensional systems with complex dynamics, such as oceans or atmospheres. In this work, we introduce score-based data assimilation for trajectory inference. We learn a score-based generative model of state trajectories based on the key insight that the score of an arbitrarily long trajectory can be decomposed into a series of scores over short segments. After training, inference is carried out using the score model, in a non-autoregressive manner by generating all states simultaneously. Quite distinctively, we decouple the observation model from the training procedure and use it only at inference to guide the generative process, which enables a wide range of zero-shot observation scenarios. We present theoretical and empirical evidence supporting the effectiveness of our method.

Latent space EBMs, also known as energy-based priors, have drawn growing interests in the field of generative modeling due to its flexibility in the formulation and strong modeling power of the latent space. However, the common practice of learning latent space EBMs with non-convergent short-run MCMC for prior and posterior sampling is hindering the model from further progress; the degenerate MCMC sampling quality in practice often leads to degraded generation quality and instability in training, especially with highly multi-modal and/or high-dimensional target distributions. To remedy this sampling issue, in this paper we introduce a simple but effective diffusion-based amortization method for long-run MCMC sampling and develop a novel learning algorithm for the latent space EBM based on it. We provide theoretical evidence that the learned amortization of MCMC is a valid long-run MCMC sampler. Experiments on several image modeling benchmark datasets demonstrate the superior performance of our method compared with strong counterparts.

This paper addresses the task of 3D pose estimation for a hand interacting with an object from a single image observation. When modeling hand-object interaction, previous works mainly exploit proximity cues, while overlooking the dynamical nature that the hand must stably grasp the object to counteract gravity and thus preventing the object from slipping or falling. These works fail to leverage dynamical constraints in the estimation and consequently often produce unstable results. Meanwhile, refining unstable configurations with physics-based reasoning remains challenging, both by the complexity of contact dynamics and by the lack of effective and efficient physics inference in the data-driven learning framework. To address both issues, we present DeepSimHO: a novel deep-learning pipeline that combines forward physics simulation and backward gradient approximation with a neural network. Specifically, for an initial hand-object pose estimated by a base network, we forward it to a physics simulator to evaluate its stability. However, due to non-smooth contact geometry and penetration, existing differentiable simulators can not provide reliable state gradient. To remedy this, we further introduce a deep network to learn the stability evaluation process from the simulator, while smoothly approximating its gradient and thus enabling effective back-propagation. Extensive experiments show that our method noticeably improves the stability of the estimation and achieves superior efficiency over test-time optimization. The code is available at https://github.com/rongakowang/DeepSimHO.

Online A/B tests have become increasingly popular and important for social platforms. However, accurately estimating the global average treatment effect (GATE) has proven to be challenging due to network interference, which violates the Stable Unit Treatment Value Assumption (SUTVA) and poses great challenge to experimental design. Existing network experimental design research was mostly based on the unbiased Horvitz-Thompson (HT) estimator with substantial data trimming to ensure unbiasedness at the price of high resultant estimation variance. In this paper, we strive to balance the bias and variance in designing randomized network experiments. Under a potential outcome model with 1-hop interference, we derive the bias and variance of the standard HT estimator and reveal their relation to the network topological structure and the covariance of the treatment assignment vector. We then propose to formulate the experimental design problem as to optimize the covariance matrix of the treatment assignment vector to achieve the bias and variance balance by minimizing the mean squared error (MSE) of the estimator. An efficient projected gradient descent algorithm is presented to the implement of the desired randomization scheme. Finally, we carry out extensive simulation studies to demonstrate the advantages of our proposed method over other existing methods in many settings, with different levels of model misspecification.

Neural SDEs are continuous-time generative models for sequential data. State-of-the-art performance for irregular time series generation has been previously obtained by training these models adversarially as GANs. However, as typical for GAN architectures, training is notoriously unstable, often suffers from mode collapse, and requires specialised techniques such as weight clipping and gradient penalty to mitigate these issues. In this paper, we introduce a novel class of scoring rules on pathspace based on signature kernels and use them as objective for training Neural SDEs non-adversarially. By showing strict properness of such kernel scores and consistency of the corresponding estimators, we provide existence and uniqueness guarantees for the minimiser. With this formulation, evaluating the generator-discriminator pair amounts to solving a system of linear path-dependent PDEs which allows for memory-efficient adjoint-based backpropagation. Moreover, because the proposed kernel scores are well-defined for paths with values in infinite dimensional spaces of functions, our framework can be easily extended to generate spatiotemporal data. Our procedure significantly outperforms alternative ways of training Neural SDEs on a variety of tasks including the simulation of rough volatility models, the conditional probabilistic forecasts of real-world forex pairs where the conditioning variable is an observed past trajectory, and the mesh-free generation of limit order book dynamics.

Real-world time series are characterized by intrinsic non-stationarity that poses a principal challenge for deep forecasting models. While previous models suffer from complicated series variations induced by changing temporal distribution, we tackle non-stationary time series with modern Koopman theory that fundamentally considers the underlying time-variant dynamics. Inspired by Koopman theory of portraying complex dynamical systems, we disentangle time-variant and time-invariant components from intricate non-stationary series by Fourier Filter and design Koopman Predictor to advance respective dynamics forward. Technically, we propose Koopa as a novel Koopman forecaster composed of stackable blocks that learn hierarchical dynamics. Koopa seeks measurement functions for Koopman embedding and utilizes Koopman operators as linear portraits of implicit transition. To cope with time-variant dynamics that exhibits strong locality, Koopa calculates context-aware operators in the temporal neighborhood and is able to utilize incoming ground truth to scale up forecast horizon. Besides, by integrating Koopman Predictors into deep residual structure, we ravel out the binding reconstruction loss in previous Koopman forecasters and achieve end-to-end forecasting objective optimization. Compared with the state-of-the-art model, Koopa achieves competitive performance while saving 77.3% training time and 76.0% memory.

Neural ordinary differential equations (neural ODEs) are a popular family of continuous-depth deep learning models. In this work, we consider a large family of parameterized ODEs with continuous-in-time parameters, which include time-dependent neural ODEs. We derive a generalization bound for this class by a Lipschitz-based argument. By leveraging the analogy between neural ODEs and deep residual networks, our approach yields in particular a generalization bound for a class of deep residual networks. The bound involves the magnitude of the difference between successive weight matrices. We illustrate numerically how this quantity affects the generalization capability of neural networks.

Modeling interacting dynamical systems, such as fluid dynamics and intermolecular interactions, is a fundamental research problem for understanding and simulating complex real-world systems. Many of these systems can be naturally represented by dynamic graphs, and graph neural network-based approaches have been proposed and shown promising performance. However, most of these approaches assume the underlying dynamics does not change over time, which is unfortunately untrue. For example, a molecular dynamics can be affected by the environment temperature over the time. In this paper, we take an attempt to provide a probabilistic view for time-varying dynamics and propose a model Context-attended Graph ODE (CARE) for modeling time-varying interacting dynamical systems. In our CARE, we explicitly use a context variable to model time-varying environment and construct an encoder to initialize the context variable from historical trajectories. Furthermore, we employ a neural ODE model to depict the dynamic evolution of the context variable inferred from system states. This context variable is incorporated into a coupled ODE to simultaneously drive the evolution of systems. Comprehensive experiments on four datasets demonstrate the effectiveness of our proposed CARE compared with several state-of-the-art approaches.

Discovering causal relationship using multivariate functional data has received a significant amount of attention very recently. In this article, we introduce a functional linear structural equation model for causal structure learning when the underlying graph involving the multivariate functions may have cycles. To enhance interpretability, our model involves a low-dimensional causal embedded space such that all the relevant causal information in the multivariate functional data is preserved in this lower-dimensional subspace. We prove that the proposed model is causally identifiable under standard assumptions that are often made in the causal discovery literature. To carry out inference of our model, we develop a fully Bayesian framework with suitable prior specifications and uncertainty quantification through posterior summaries. We illustrate the superior performance of our method over existing methods in terms of causal graph estimation through extensive simulation studies. We also demonstrate the proposed method using a brain EEG dataset.

Survival or time-to-event data with time-varying covariates are common in practice, and exploring the non-stationarity in covariates is essential to accurately analyzing the nonlinear dependence of time-to-event outcomes on covariates. Traditional survival analysis methods such as Cox proportional hazards model have been extended to address the time-varying covariates through a counting process formulation, although sophisticated machine learning methods that can accommodate time-varying covariates have been limited. In this paper, we propose a non-parametric Bayesian survival model to analyze the nonlinear dependence of time-to-event outcomes on time-varying covariates. We focus on a computationally feasible Cox process called permanental process, which assumes the square root of hazard function to be generated from a Gaussian process, and tailor it for survival data with time-varying covariates. We verify that the proposed model holds with the representer theorem, a beneficial property for functional analysis, which offers us a fast Bayesian estimation algorithm that scales linearly with the number of observed events without relying on Markov Chain Monte Carlo computation. We evaluate our algorithm on synthetic and real-world data, and show that it achieves comparable predictive accuracy while being tens to hundreds of times faster than state-of-the-art methods.

Uncertainty estimation is an important research area to make deep neural networks (DNNs) more trustworthy. While extensive research on uncertainty estimation has been conducted with unimodal data, uncertainty estimation for multimodal data remains a challenge. Neural processes (NPs) have been demonstrated to be an effective uncertainty estimation method for unimodal data by providing the reliability of Gaussian processes with efficient and powerful DNNs. While NPs hold significant potential for multimodal uncertainty estimation, the adaptation of NPs for multimodal data has not been carefully studied. To bridge this gap, we propose Multimodal Neural Processes (MNPs) by generalising NPs for multimodal uncertainty estimation. Based on the framework of NPs, MNPs consist of several novel and principled mechanisms tailored to the characteristics of multimodal data. In extensive empirical evaluation, our method achieves state-of-the-art multimodal uncertainty estimation performance, showing its appealing robustness against noisy samples and reliability in out-of-distribution detection with faster computation time compared to the current state-of-the-art multimodal uncertainty estimation method.

Existing regression models tend to fall short in both accuracy and uncertainty estimation when the label distribution is imbalanced. In this paper, we propose a probabilistic deep learning model, dubbed variational imbalanced regression (VIR), which not only performs well in imbalanced regression but naturally produces reasonable uncertainty estimation as a byproduct. Different from typical variational autoencoders assuming I.I.D. representations (a data point's representation is not directly affected by other data points), our VIR borrows data with similar regression labels to compute the latent representation's variational distribution; furthermore, different from deterministic regression models producing point estimates, VIR predicts the entire normal-inverse-gamma distributions and modulates the associated conjugate distributions to impose probabilistic reweighting on the imbalanced data, thereby providing better uncertainty estimation. Experiments in several real-world datasets show that our VIR can outperform state-of-the-art imbalanced regression models in terms of both accuracy and uncertainty estimation. Code will soon be available at https://github.com/Wang-ML-Lab/variational-imbalanced-regression.

We present an alternative approach to decompose non-negative tensors, called many-body approximation. Traditional decomposition methods assume low-rankness in the representation, resulting in difficulties in global optimization and target rank selection. We avoid these problems by energy-based modeling of tensors, where a tensor and its mode correspond to a probability distribution and a random variable, respectively. Our model can be globally optimized in terms of the KL divergence minimization by taking the interaction between variables (that is, modes), into account that can be tuned more intuitively than ranks. Furthermore, we visualize interactions between modes as tensor networks and reveal a nontrivial relationship between many-body approximation and low-rank approximation. We demonstrate the effectiveness of our approach in tensor completion and approximation.

Sparse deep learning has become a popular technique for improving the performance of deep neural networks in areas such as uncertainty quantification, variable selection, and large-scale network compression. However, most existing research has focused on problems where the observations are independent and identically distributed (i.i.d.), and there has been little work on the problems where the observations are dependent, such as time series data and sequential data in natural language processing. This paper aims to address this gap by studying the theory for sparse deep learning with dependent data. We show that sparse recurrent neural networks (RNNs) can be consistently estimated, and their predictions are asymptotically normally distributed under appropriate assumptions, enabling the prediction uncertainty to be correctly quantified. Our numerical results show that sparse deep learning outperforms state-of-the-art methods, such as conformal predictions, in prediction uncertainty quantification for time series data. Furthermore, our results indicate that the proposed method can consistently identify the autoregressive order for time series data and outperform existing methods in large-scale model compression. Our proposed method has important practical implications in fields such as finance, healthcare, and energy, where both accurate point estimates and prediction uncertainty quantification are of concern.

In disentangled representation learning, a model is asked to tease apart a dataset's underlying sources of variation and represent them independently of one another. Since the model is provided with no ground truth information about these sources, inductive biases take a paramount role in enabling disentanglement. In this work, we construct an inductive bias towards encoding to and decoding from an organized latent space. Concretely, we do this by (i) quantizing the latent space into discrete code vectors with a separate learnable scalar codebook per dimension and (ii) applying strong model regularization via an unusually high weight decay. Intuitively, the latent space design forces the encoder to combinatorially construct codes from a small number of distinct scalar values, which in turn enables the decoder to assign a consistent meaning to each value. Regularization then serves to drive the model towards this parsimonious strategy. We demonstrate the broad applicability of this approach by adding it to both basic data-reconstructing (vanilla autoencoder) and latent-reconstructing (InfoGAN) generative models. For reliable evaluation, we also propose InfoMEC, a new set of metrics for disentanglement that is cohesively grounded in information theory and fixes well-established shortcomings in previous metrics. Together with regularization, latent quantization dramatically improves the modularity and explicitness of learned representations on a representative suite of benchmark datasets. In particular, our quantized-latent autoencoder (QLAE) consistently outperforms strong methods from prior work in these key disentanglement properties without compromising data reconstruction.

The neural network structures of generative models and their corresponding inference models paired in variational autoencoders (VAEs) play a critical role in the models' generative performance. However, powerful VAE network structures are hand-crafted and fixed prior to training, resulting in a one-size-fits-all approach that requires heavy computation to tune for given data. Moreover, existing VAE regularization methods largely overlook the importance of network structures and fail to prevent overfitting in deep VAE models with cascades of hidden layers. To address these issues, we propose a Bayesian inference framework that automatically adapts VAE network structures to data and prevent overfitting as they grow deeper. We model the number of hidden layers with a beta process to infer the most plausible encoding/decoding network depths warranted by data and perform layer-wise dropout regularization with a conjugate Bernoulli process. We develop a scalable estimator that performs joint inference on both VAE network structures and latent variables. Our experiments show that the inference framework effectively prevents overfitting in both shallow and deep VAE models, yielding state-of-the-art performance. We demonstrate that our framework is compatible with different types of VAE backbone networks and can be applied to various VAE variants, further improving their performance.

A fundamental problem in many sciences is the learning of causal structure underlying a system, typically through observation and experimentation. Commonly, one even collects data across multiple domains, such as gene sequencing from different labs, or neural recordings from different species. Although there exist methods for learning the equivalence class of causal diagrams from observational and experimental data, they are meant to operate in a single domain. In this paper, we develop a fundamental approach to structure learning in non-Markovian systems (i.e. when there exist latent confounders) leveraging observational and interventional data collected from multiple domains. Specifically, we start by showing that learning from observational data in multiple domains is equivalent to learning from interventional data with unknown targets in a single domain. But there are also subtleties when considering observational and experimental data. Using causal invariances derived from do-calculus, we define a property called S-Markov that connects interventional distributions from multiple-domains to graphical criteria on a selection diagram. Leveraging the S-Markov property, we introduce a new constraint-based causal discovery algorithm, S-FCI, that can learn from observational and interventional data from different domains. We prove that the algorithm is sound and subsumes existing constraint-based causal discovery algorithms.